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- xavier
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12 years 10 months ago #685
by xavier
It is a bit difficult to give a recipe by email. You should have a look at the different papers on the force field development (listed in the Publications link at the top of he page) to get a good idea o how to proceed as a general manner.
Then to generate a CG topology you generally start by a atomistic topology that you simplify and then define the bonded and non-bonded terms by successive refinement steps designed to reproduce experimental and atomistic simulations data.
There is a tutorial soon ... check the home page.
Replied by xavier on topic newbies in CGMD
In other words you'd like to generate both fine grain (atomistic) and coarse grain topologies?syahidah wrote: hi sir,
i did tutorial for g_fg2cg
however,i'm little bit wondering on how we can get the cg.gro file for the molecules that is not included in the forcefield library.meaning that, if molecules like dupc and dspc, they are already have the topology in the martini.itp,but how about the other molecule? i'm wondering is there any steps to produce *_fg.itp to *_cg.itp?
It is a bit difficult to give a recipe by email. You should have a look at the different papers on the force field development (listed in the Publications link at the top of he page) to get a good idea o how to proceed as a general manner.
Then to generate a CG topology you generally start by a atomistic topology that you simplify and then define the bonded and non-bonded terms by successive refinement steps designed to reproduce experimental and atomistic simulations data.
There is a tutorial soon ... check the home page.
thank you sir,
your reply much aprreciated sir.
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- syahidah
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12 years 10 months ago #690
by syahidah
Replied by syahidah on topic newbies in CGMD
does it mean u will upload the tutorial for this step soon?
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12 years 10 months ago #691
by xavier
md.chem.rug.nl/cgmartini/index.php/compo...e-graining-workshop-
Replied by xavier on topic newbies in CGMD
syahidah wrote: does it mean u will upload the tutorial for this step soon?
md.chem.rug.nl/cgmartini/index.php/compo...e-graining-workshop-
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12 years 10 months ago #694
by syahidah
Replied by syahidah on topic newbies in CGMD
sir,
if you don't mind, may i ask for the correct output file (cg.gro) from the refine tutorial,
where,
when i do the transformation of fg to dg by using these commands;
g_fg2cg -pfg fg.top -pcg cg.top -c fg.gro -n 1 -o cg.gro
g_fg2cg -pfg fg.top -pcg cg.top -c fg.xtc -n 1 -o fg2cg.xtc
however, the output file seems not complete.
so may i have the correct one.so i can determine what's the problem with mine.
thank you sir.
if you don't mind, may i ask for the correct output file (cg.gro) from the refine tutorial,
where,
when i do the transformation of fg to dg by using these commands;
g_fg2cg -pfg fg.top -pcg cg.top -c fg.gro -n 1 -o cg.gro
g_fg2cg -pfg fg.top -pcg cg.top -c fg.xtc -n 1 -o fg2cg.xtc
however, the output file seems not complete.
so may i have the correct one.so i can determine what's the problem with mine.
thank you sir.
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- syahidah
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12 years 10 months ago #695
by syahidah
Replied by syahidah on topic newbies in CGMD
sir,
in dupc_fg.itp file in the refine tutorial,there is [mapping] section. how did you produce this?and how did you get your topology for atomtype,bonds etc?because for my case i use prodrg and antechamber (amber8).
thank you sir.
in dupc_fg.itp file in the refine tutorial,there is [mapping] section. how did you produce this?and how did you get your topology for atomtype,bonds etc?because for my case i use prodrg and antechamber (amber8).
thank you sir.
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12 years 10 months ago #698
by xavier
You should read the paper introducing the reverse transformation. The manner to define the mapping is explained (I suppose).
Then to generate your own you should have a look at the files in the tutorial. They would guide you on the manner to define the mapping atomistic to CG ...
XAvier.
Replied by xavier on topic newbies in CGMD
syahidah wrote: sir,
in dupc_fg.itp file in the refine tutorial,there is [mapping] section. how did you produce this?and how did you get your topology for atomtype,bonds etc?because for my case i use prodrg and antechamber (amber8).
thank you sir.
You should read the paper introducing the reverse transformation. The manner to define the mapping is explained (I suppose).
Then to generate your own you should have a look at the files in the tutorial. They would guide you on the manner to define the mapping atomistic to CG ...
XAvier.
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12 years 10 months ago #699
by syahidah
Replied by syahidah on topic newbies in CGMD
sir,
would you mine to share with me the paper?
i've gone through the paper "The MARTINI force field: coarse grained model for biomolecular simulations"
however,i'm still not completely get it.if u have the correct one, i mean the output from the refine part tutorial which is the dupc_cg.gro,would u mind to share with me?
thank you so much sir.
would you mine to share with me the paper?
i've gone through the paper "The MARTINI force field: coarse grained model for biomolecular simulations"
however,i'm still not completely get it.if u have the correct one, i mean the output from the refine part tutorial which is the dupc_cg.gro,would u mind to share with me?
thank you so much sir.
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12 years 10 months ago #700
by xavier
I'll see where to find this file. I guess it is not given within the tutorial?
Replied by xavier on topic newbies in CGMD
syahidah wrote: sir,
would you mine to share with me the paper?
i've gone through the paper "The MARTINI force field: coarse grained model for biomolecular simulations"
however,i'm still not completely get it.if u have the correct one, i mean the output from the refine part tutorial which is the dupc_cg.gro,would u mind to share with me?
thank you so much sir.
I'll see where to find this file. I guess it is not given within the tutorial?
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12 years 10 months ago #701
by syahidah
Replied by syahidah on topic newbies in CGMD
if it is in you tutorial,meaning that it's the one that i read now.i will read it carefully sir.
sir, may i contact you directly through your email?
sir, may i contact you directly through your email?
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12 years 10 months ago #702
by syahidah
Replied by syahidah on topic newbies in CGMD
do you mean the file for ouput.no,there is no output files for the refine tutorial.
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12 years 10 months ago #703
by xavier
I do not understand your problem! There is no need of a dupc_cg.gro file! Is it supposed to be dppc_cg.gro?
XAvier.
PS: It is preferable to keep the discussion on the forum.
Replied by xavier on topic newbies in CGMD
syahidah wrote: do you mean the file for ouput.no,there is no output files for the refine tutorial.
I do not understand your problem! There is no need of a dupc_cg.gro file! Is it supposed to be dppc_cg.gro?
XAvier.
PS: It is preferable to keep the discussion on the forum.
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12 years 10 months ago #704
by syahidah
Replied by syahidah on topic newbies in CGMD
sir,i'm sorry for all these.
actually,i'm doing the refine tutorial which is included in lipid_tutorial.tar.gz which is in refine folder, the sample structure is dupc.
i am so sorry,sir.
actually,i'm doing the refine tutorial which is included in lipid_tutorial.tar.gz which is in refine folder, the sample structure is dupc.
i am so sorry,sir.
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12 years 10 months ago #713
by xavier
Ok, I localized the tutorial that you are doing. I am not familiar with it but the command you are running should basically work fine. May be you could detail what is going wrong in the production of the file.
XAvier,
Replied by xavier on topic newbies in CGMD
syahidah wrote: do you mean the file for ouput.no,there is no output files for the refine tutorial.
Ok, I localized the tutorial that you are doing. I am not familiar with it but the command you are running should basically work fine. May be you could detail what is going wrong in the production of the file.
XAvier,
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12 years 9 months ago #738
by syahidah
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sir,
i did for my own dppc molecule where i draw it by using avogadro.i got the topology from the dundee prodrg where i submit the dppc.pdb file (without H).then i do the [mapping by use the tutorial .itp file for dppc as guidance.then i ran the g_fg2cg with command :g_fg2cg -pfg fg.top -pcg cg.top -c fg.gro -n 1 -o cg.gro
the result obtained is:
DPPC molecules in water
12
1DPPC NC3 1 2.959 0.930 -1.476
1DPPC PO4 2 4.878 1.239 -1.626
1DPPC GL1 3 5.001 1.397 -2.107
1DPPC GL2 4 4.500 1.418 -2.541
1DPPC C1A 5 3.000 1.326 -2.958
1DPPC C2A 6 6.500 1.265 -3.351
1DPPC C3A 7 2.474 1.395 -3.791
1DPPC C4A 8 6.058 1.567 -1.631
1DPPC C1B 9 3.000 1.929 -1.380
1DPPC C2B 10 4.500 2.311 -1.141
1DPPC C3B 11 6.000 2.723 -0.885
1DPPC C4B 12 2.526 3.061 -0.651
0.00000 0.00000 0.00000
so may i check with you,do my result is correct?
may i know whether we can use the charge that we get from the dundee prodrg output (.itp file) for the molecule, or we need to run special process for charge calculation (for example: RESP program) to replace the charge in .itp file?
besides, would you mine to show me how you do coarse-graining for this molecule;
[ moleculetype ]
; Name nrexcl
LIG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 LIG OAQ 1 -0.720 15.9994
2 C 1 LIG CAP 1 0.383 12.0110
3 OM 1 LIG OAR 1 -0.720 15.9994
4 CH2 1 LIG CAO 1 0.071 14.0270
5 CB 1 LIG CAC 1 -0.014 12.0110
6 CR61 1 LIG CAA 2 -0.035 13.0190
7 CR61 1 LIG CAB 2 -0.035 13.0190
8 CR61 1 LIG CAD 2 -0.035 13.0190
9 CR61 1 LIG CAE 2 -0.036 13.0190
10 CB 1 LIG CAF 2 0.141 12.0110
11 N 1 LIG NAG 3 0.000 14.0067
12 H 1 LIG HAA 3 0.000 1.0080
13 CB 1 LIG CAH 4 0.141 12.0110
14 CR61 1 LIG CAI 4 -0.035 13.0190
15 CR61 1 LIG CAK 4 -0.035 13.0190
16 CR61 1 LIG CAM 4 -0.036 13.0190
17 CR61 1 LIG CAL 4 -0.035 13.0190
18 CB 1 LIG CAJ 5 0.000 12.0110
19 CL 1 LIG CLAN 5 0.000 35.4530
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.125 418400.0 0.125 418400.0 ; OAQ CAP
2 3 1 0.125 418400.0 0.125 418400.0 ; CAP OAR
2 4 1 0.153 334720.0 0.153 334720.0 ; CAP CAO
4 5 1 0.153 334720.0 0.153 334720.0 ; CAO CAC
5 6 1 0.139 418400.0 0.139 418400.0 ; CAC CAA
5 10 1 0.139 418400.0 0.139 418400.0 ; CAC CAF
6 7 1 0.139 418400.0 0.139 418400.0 ; CAA CAB
7 8 1 0.139 418400.0 0.139 418400.0 ; CAB CAD
8 9 1 0.139 418400.0 0.139 418400.0 ; CAD CAE
9 10 1 0.139 418400.0 0.139 418400.0 ; CAE CAF
10 11 1 0.133 376560.0 0.133 376560.0 ; CAF NAG
11 12 1 0.100 374468.0 0.100 374468.0 ; NAG HAA
11 13 1 0.133 376560.0 0.133 376560.0 ; NAG CAH
13 14 1 0.139 418400.0 0.139 418400.0 ; CAH CAI
13 18 1 0.139 418400.0 0.139 418400.0 ; CAH CAJ
14 15 1 0.139 418400.0 0.139 418400.0 ; CAI CAK
15 16 1 0.139 418400.0 0.139 418400.0 ; CAK CAM
16 17 1 0.139 418400.0 0.139 418400.0 ; CAM CAL
17 18 1 0.139 418400.0 0.139 418400.0 ; CAL CAJ
18 19 1 0.173 423128.4 0.173 423128.4 ; CAJ CLAN
[ pairs ]
; ai aj fu c0, c1, ...
1 5 1 ; OAQ CAC
2 6 1 ; CAP CAA
2 10 1 ; CAP CAF
3 5 1 ; OAR CAC
4 7 1 ; CAO CAB
4 9 1 ; CAO CAE
4 11 1 ; CAO NAG
5 8 1 ; CAC CAD
5 12 1 ; CAC HAA
5 13 1 ; CAC CAH
6 9 1 ; CAA CAE
6 11 1 ; CAA NAG
7 10 1 ; CAB CAF
8 11 1 ; CAD NAG
9 12 1 ; CAE HAA
9 13 1 ; CAE CAH
10 14 1 ; CAF CAI
10 18 1 ; CAF CAJ
11 15 1 ; NAG CAK
11 17 1 ; NAG CAL
11 19 1 ; NAG CLAN
12 14 1 ; HAA CAI
12 18 1 ; HAA CAJ
13 16 1 ; CAH CAM
14 17 1 ; CAI CAL
14 19 1 ; CAI CLAN
15 18 1 ; CAK CAJ
16 19 1 ; CAM CLAN
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 1 126.0 502.1 126.0 502.1 ; OAQ CAP OAR
1 2 4 1 117.0 502.1 117.0 502.1 ; OAQ CAP CAO
3 2 4 1 117.0 502.1 117.0 502.1 ; OAR CAP CAO
2 4 5 1 109.5 460.2 109.5 460.2 ; CAP CAO CAC
4 5 6 1 120.0 418.4 120.0 418.4 ; CAO CAC CAA
4 5 10 1 126.0 418.4 126.0 418.4 ; CAO CAC CAF
6 5 10 1 120.0 418.4 120.0 418.4 ; CAA CAC CAF
5 6 7 1 120.0 418.4 120.0 418.4 ; CAC CAA CAB
6 7 8 1 120.0 418.4 120.0 418.4 ; CAA CAB CAD
7 8 9 1 120.0 418.4 120.0 418.4 ; CAB CAD CAE
8 9 10 1 120.0 418.4 120.0 418.4 ; CAD CAE CAF
5 10 9 1 120.0 418.4 120.0 418.4 ; CAC CAF CAE
5 10 11 1 120.0 418.4 120.0 418.4 ; CAC CAF NAG
9 10 11 1 120.0 418.4 120.0 418.4 ; CAE CAF NAG
10 11 12 1 120.0 418.4 120.0 418.4 ; CAF NAG HAA
10 11 13 1 120.0 418.4 120.0 418.4 ; CAF NAG CAH
12 11 13 1 120.0 418.4 120.0 418.4 ; HAA NAG CAH
11 13 14 1 120.0 418.4 120.0 418.4 ; NAG CAH CAI
11 13 18 1 120.0 418.4 120.0 418.4 ; NAG CAH CAJ
14 13 18 1 120.0 418.4 120.0 418.4 ; CAI CAH CAJ
13 14 15 1 120.0 418.4 120.0 418.4 ; CAH CAI CAK
14 15 16 1 120.0 418.4 120.0 418.4 ; CAI CAK CAM
15 16 17 1 120.0 418.4 120.0 418.4 ; CAK CAM CAL
16 17 18 1 120.0 418.4 120.0 418.4 ; CAM CAL CAJ
13 18 17 1 120.0 418.4 120.0 418.4 ; CAH CAJ CAL
13 18 19 1 120.0 418.4 120.0 418.4 ; CAH CAJ CLAN
17 18 19 1 120.0 418.4 120.0 418.4 ; CAL CAJ CLAN
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 4 3 1 2 0.0 1673.6 0.0 1673.6 ; imp CAP CAO OAR OAQ
5 10 6 4 2 0.0 1673.6 0.0 1673.6 ; imp CAC CAF CAA CAO
10 5 11 9 2 0.0 1673.6 0.0 1673.6 ; imp CAF CAC NAG CAE
11 10 12 13 2 0.0 1673.6 0.0 1673.6 ; imp NAG CAF HAA CAH
13 11 18 14 2 0.0 1673.6 0.0 1673.6 ; imp CAH NAG CAJ CAI
18 13 19 17 2 0.0 1673.6 0.0 1673.6 ; imp CAJ CAH CLAN CAL
13 14 15 16 2 0.0 1673.6 0.0 1673.6 ; imp CAH CAI CAK CAM
14 15 16 17 2 0.0 1673.6 0.0 1673.6 ; imp CAI CAK CAM CAL
15 16 17 18 2 0.0 1673.6 0.0 1673.6 ; imp CAK CAM CAL CAJ
16 17 18 13 2 0.0 1673.6 0.0 1673.6 ; imp CAM CAL CAJ CAH
17 18 13 14 2 0.0 1673.6 0.0 1673.6 ; imp CAL CAJ CAH CAI
18 13 14 15 2 0.0 1673.6 0.0 1673.6 ; imp CAJ CAH CAI CAK
5 6 7 8 2 0.0 1673.6 0.0 1673.6 ; imp CAC CAA CAB CAD
6 7 8 9 2 0.0 1673.6 0.0 1673.6 ; imp CAA CAB CAD CAE
7 8 9 10 2 0.0 1673.6 0.0 1673.6 ; imp CAB CAD CAE CAF
8 9 10 5 2 0.0 1673.6 0.0 1673.6 ; imp CAD CAE CAF CAC
9 10 5 6 2 0.0 1673.6 0.0 1673.6 ; imp CAE CAF CAC CAA
10 5 6 7 2 0.0 1673.6 0.0 1673.6 ; imp CAF CAC CAA CAB
5 4 2 1 1 0.0 0.4 6 0.0 0.4 6 ; dih CAC CAO CAP OAQ
10 5 4 2 1 0.0 0.4 6 0.0 0.4 6 ; dih CAF CAC CAO CAP
5 10 11 13 1 180.0 33.5 2 180.0 33.5 2 ; dih CAC CAF NAG CAH
10 11 13 18 1 180.0 33.5 2 180.0 33.5 2 ; dih CAF NAG CAH CAJ
sir,your help is most appreciated.
thank you.
i did for my own dppc molecule where i draw it by using avogadro.i got the topology from the dundee prodrg where i submit the dppc.pdb file (without H).then i do the [mapping by use the tutorial .itp file for dppc as guidance.then i ran the g_fg2cg with command :g_fg2cg -pfg fg.top -pcg cg.top -c fg.gro -n 1 -o cg.gro
the result obtained is:
DPPC molecules in water
12
1DPPC NC3 1 2.959 0.930 -1.476
1DPPC PO4 2 4.878 1.239 -1.626
1DPPC GL1 3 5.001 1.397 -2.107
1DPPC GL2 4 4.500 1.418 -2.541
1DPPC C1A 5 3.000 1.326 -2.958
1DPPC C2A 6 6.500 1.265 -3.351
1DPPC C3A 7 2.474 1.395 -3.791
1DPPC C4A 8 6.058 1.567 -1.631
1DPPC C1B 9 3.000 1.929 -1.380
1DPPC C2B 10 4.500 2.311 -1.141
1DPPC C3B 11 6.000 2.723 -0.885
1DPPC C4B 12 2.526 3.061 -0.651
0.00000 0.00000 0.00000
so may i check with you,do my result is correct?
may i know whether we can use the charge that we get from the dundee prodrg output (.itp file) for the molecule, or we need to run special process for charge calculation (for example: RESP program) to replace the charge in .itp file?
besides, would you mine to show me how you do coarse-graining for this molecule;
[ moleculetype ]
; Name nrexcl
LIG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 LIG OAQ 1 -0.720 15.9994
2 C 1 LIG CAP 1 0.383 12.0110
3 OM 1 LIG OAR 1 -0.720 15.9994
4 CH2 1 LIG CAO 1 0.071 14.0270
5 CB 1 LIG CAC 1 -0.014 12.0110
6 CR61 1 LIG CAA 2 -0.035 13.0190
7 CR61 1 LIG CAB 2 -0.035 13.0190
8 CR61 1 LIG CAD 2 -0.035 13.0190
9 CR61 1 LIG CAE 2 -0.036 13.0190
10 CB 1 LIG CAF 2 0.141 12.0110
11 N 1 LIG NAG 3 0.000 14.0067
12 H 1 LIG HAA 3 0.000 1.0080
13 CB 1 LIG CAH 4 0.141 12.0110
14 CR61 1 LIG CAI 4 -0.035 13.0190
15 CR61 1 LIG CAK 4 -0.035 13.0190
16 CR61 1 LIG CAM 4 -0.036 13.0190
17 CR61 1 LIG CAL 4 -0.035 13.0190
18 CB 1 LIG CAJ 5 0.000 12.0110
19 CL 1 LIG CLAN 5 0.000 35.4530
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.125 418400.0 0.125 418400.0 ; OAQ CAP
2 3 1 0.125 418400.0 0.125 418400.0 ; CAP OAR
2 4 1 0.153 334720.0 0.153 334720.0 ; CAP CAO
4 5 1 0.153 334720.0 0.153 334720.0 ; CAO CAC
5 6 1 0.139 418400.0 0.139 418400.0 ; CAC CAA
5 10 1 0.139 418400.0 0.139 418400.0 ; CAC CAF
6 7 1 0.139 418400.0 0.139 418400.0 ; CAA CAB
7 8 1 0.139 418400.0 0.139 418400.0 ; CAB CAD
8 9 1 0.139 418400.0 0.139 418400.0 ; CAD CAE
9 10 1 0.139 418400.0 0.139 418400.0 ; CAE CAF
10 11 1 0.133 376560.0 0.133 376560.0 ; CAF NAG
11 12 1 0.100 374468.0 0.100 374468.0 ; NAG HAA
11 13 1 0.133 376560.0 0.133 376560.0 ; NAG CAH
13 14 1 0.139 418400.0 0.139 418400.0 ; CAH CAI
13 18 1 0.139 418400.0 0.139 418400.0 ; CAH CAJ
14 15 1 0.139 418400.0 0.139 418400.0 ; CAI CAK
15 16 1 0.139 418400.0 0.139 418400.0 ; CAK CAM
16 17 1 0.139 418400.0 0.139 418400.0 ; CAM CAL
17 18 1 0.139 418400.0 0.139 418400.0 ; CAL CAJ
18 19 1 0.173 423128.4 0.173 423128.4 ; CAJ CLAN
[ pairs ]
; ai aj fu c0, c1, ...
1 5 1 ; OAQ CAC
2 6 1 ; CAP CAA
2 10 1 ; CAP CAF
3 5 1 ; OAR CAC
4 7 1 ; CAO CAB
4 9 1 ; CAO CAE
4 11 1 ; CAO NAG
5 8 1 ; CAC CAD
5 12 1 ; CAC HAA
5 13 1 ; CAC CAH
6 9 1 ; CAA CAE
6 11 1 ; CAA NAG
7 10 1 ; CAB CAF
8 11 1 ; CAD NAG
9 12 1 ; CAE HAA
9 13 1 ; CAE CAH
10 14 1 ; CAF CAI
10 18 1 ; CAF CAJ
11 15 1 ; NAG CAK
11 17 1 ; NAG CAL
11 19 1 ; NAG CLAN
12 14 1 ; HAA CAI
12 18 1 ; HAA CAJ
13 16 1 ; CAH CAM
14 17 1 ; CAI CAL
14 19 1 ; CAI CLAN
15 18 1 ; CAK CAJ
16 19 1 ; CAM CLAN
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 1 126.0 502.1 126.0 502.1 ; OAQ CAP OAR
1 2 4 1 117.0 502.1 117.0 502.1 ; OAQ CAP CAO
3 2 4 1 117.0 502.1 117.0 502.1 ; OAR CAP CAO
2 4 5 1 109.5 460.2 109.5 460.2 ; CAP CAO CAC
4 5 6 1 120.0 418.4 120.0 418.4 ; CAO CAC CAA
4 5 10 1 126.0 418.4 126.0 418.4 ; CAO CAC CAF
6 5 10 1 120.0 418.4 120.0 418.4 ; CAA CAC CAF
5 6 7 1 120.0 418.4 120.0 418.4 ; CAC CAA CAB
6 7 8 1 120.0 418.4 120.0 418.4 ; CAA CAB CAD
7 8 9 1 120.0 418.4 120.0 418.4 ; CAB CAD CAE
8 9 10 1 120.0 418.4 120.0 418.4 ; CAD CAE CAF
5 10 9 1 120.0 418.4 120.0 418.4 ; CAC CAF CAE
5 10 11 1 120.0 418.4 120.0 418.4 ; CAC CAF NAG
9 10 11 1 120.0 418.4 120.0 418.4 ; CAE CAF NAG
10 11 12 1 120.0 418.4 120.0 418.4 ; CAF NAG HAA
10 11 13 1 120.0 418.4 120.0 418.4 ; CAF NAG CAH
12 11 13 1 120.0 418.4 120.0 418.4 ; HAA NAG CAH
11 13 14 1 120.0 418.4 120.0 418.4 ; NAG CAH CAI
11 13 18 1 120.0 418.4 120.0 418.4 ; NAG CAH CAJ
14 13 18 1 120.0 418.4 120.0 418.4 ; CAI CAH CAJ
13 14 15 1 120.0 418.4 120.0 418.4 ; CAH CAI CAK
14 15 16 1 120.0 418.4 120.0 418.4 ; CAI CAK CAM
15 16 17 1 120.0 418.4 120.0 418.4 ; CAK CAM CAL
16 17 18 1 120.0 418.4 120.0 418.4 ; CAM CAL CAJ
13 18 17 1 120.0 418.4 120.0 418.4 ; CAH CAJ CAL
13 18 19 1 120.0 418.4 120.0 418.4 ; CAH CAJ CLAN
17 18 19 1 120.0 418.4 120.0 418.4 ; CAL CAJ CLAN
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 4 3 1 2 0.0 1673.6 0.0 1673.6 ; imp CAP CAO OAR OAQ
5 10 6 4 2 0.0 1673.6 0.0 1673.6 ; imp CAC CAF CAA CAO
10 5 11 9 2 0.0 1673.6 0.0 1673.6 ; imp CAF CAC NAG CAE
11 10 12 13 2 0.0 1673.6 0.0 1673.6 ; imp NAG CAF HAA CAH
13 11 18 14 2 0.0 1673.6 0.0 1673.6 ; imp CAH NAG CAJ CAI
18 13 19 17 2 0.0 1673.6 0.0 1673.6 ; imp CAJ CAH CLAN CAL
13 14 15 16 2 0.0 1673.6 0.0 1673.6 ; imp CAH CAI CAK CAM
14 15 16 17 2 0.0 1673.6 0.0 1673.6 ; imp CAI CAK CAM CAL
15 16 17 18 2 0.0 1673.6 0.0 1673.6 ; imp CAK CAM CAL CAJ
16 17 18 13 2 0.0 1673.6 0.0 1673.6 ; imp CAM CAL CAJ CAH
17 18 13 14 2 0.0 1673.6 0.0 1673.6 ; imp CAL CAJ CAH CAI
18 13 14 15 2 0.0 1673.6 0.0 1673.6 ; imp CAJ CAH CAI CAK
5 6 7 8 2 0.0 1673.6 0.0 1673.6 ; imp CAC CAA CAB CAD
6 7 8 9 2 0.0 1673.6 0.0 1673.6 ; imp CAA CAB CAD CAE
7 8 9 10 2 0.0 1673.6 0.0 1673.6 ; imp CAB CAD CAE CAF
8 9 10 5 2 0.0 1673.6 0.0 1673.6 ; imp CAD CAE CAF CAC
9 10 5 6 2 0.0 1673.6 0.0 1673.6 ; imp CAE CAF CAC CAA
10 5 6 7 2 0.0 1673.6 0.0 1673.6 ; imp CAF CAC CAA CAB
5 4 2 1 1 0.0 0.4 6 0.0 0.4 6 ; dih CAC CAO CAP OAQ
10 5 4 2 1 0.0 0.4 6 0.0 0.4 6 ; dih CAF CAC CAO CAP
5 10 11 13 1 180.0 33.5 2 180.0 33.5 2 ; dih CAC CAF NAG CAH
10 11 13 18 1 180.0 33.5 2 180.0 33.5 2 ; dih CAF NAG CAH CAJ
sir,your help is most appreciated.
thank you.
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- syahidah
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12 years 9 months ago #739
by syahidah
Replied by syahidah on topic newbies in CGMD
sir,
could you show me?
because it is new molecule.
thank you, sir.
could you show me?
because it is new molecule.
thank you, sir.
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- xavier
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12 years 9 months ago #744
by xavier
Replied by xavier on topic newbies in CGMD
Well you are asking a lot of things, which makes a clear answer a bit difficult.
So:
1- the dppc CG conformation might be fine indeed. But looking at the coordinate, it seems that a few connected atoms have coordinates indicating a large distance ... more than 2 nm between them. This can not be.
2- The charges from dundee are known not to be accurate and are exclusively for atomistic structures .. so if you want to use them in the CG topology the answer is no ... do not use them. The CG topology for DPPC is available and you should not need to redo it!
3- I can not help you with the new molecule. It is quite some work to parameterize a new molecule and you should do it your self going through the different tutorials you can find on the site.
XAvier.
So:
1- the dppc CG conformation might be fine indeed. But looking at the coordinate, it seems that a few connected atoms have coordinates indicating a large distance ... more than 2 nm between them. This can not be.
2- The charges from dundee are known not to be accurate and are exclusively for atomistic structures .. so if you want to use them in the CG topology the answer is no ... do not use them. The CG topology for DPPC is available and you should not need to redo it!
3- I can not help you with the new molecule. It is quite some work to parameterize a new molecule and you should do it your self going through the different tutorials you can find on the site.
XAvier.
syahidah wrote: sir,
i did for my own dppc molecule where i draw it by using avogadro.i got the topology from the dundee prodrg where i submit the dppc.pdb file (without H).then i do the [mapping by use the tutorial .itp file for dppc as guidance.then i ran the g_fg2cg with command :g_fg2cg -pfg fg.top -pcg cg.top -c fg.gro -n 1 -o cg.gro
the result obtained is:
DPPC molecules in water
12
1DPPC NC3 1 2.959 0.930 -1.476
1DPPC PO4 2 4.878 1.239 -1.626
1DPPC GL1 3 5.001 1.397 -2.107
1DPPC GL2 4 4.500 1.418 -2.541
1DPPC C1A 5 3.000 1.326 -2.958
1DPPC C2A 6 6.500 1.265 -3.351
1DPPC C3A 7 2.474 1.395 -3.791
1DPPC C4A 8 6.058 1.567 -1.631
1DPPC C1B 9 3.000 1.929 -1.380
1DPPC C2B 10 4.500 2.311 -1.141
1DPPC C3B 11 6.000 2.723 -0.885
1DPPC C4B 12 2.526 3.061 -0.651
0.00000 0.00000 0.00000
so may i check with you,do my result is correct?
may i know whether we can use the charge that we get from the dundee prodrg output (.itp file) for the molecule, or we need to run special process for charge calculation (for example: RESP program) to replace the charge in .itp file?
besides, would you mine to show me how you do coarse-graining for this molecule;
[ moleculetype ]
; Name nrexcl
LIG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 LIG OAQ 1 -0.720 15.9994
2 C 1 LIG CAP 1 0.383 12.0110
3 OM 1 LIG OAR 1 -0.720 15.9994
4 CH2 1 LIG CAO 1 0.071 14.0270
5 CB 1 LIG CAC 1 -0.014 12.0110
6 CR61 1 LIG CAA 2 -0.035 13.0190
7 CR61 1 LIG CAB 2 -0.035 13.0190
8 CR61 1 LIG CAD 2 -0.035 13.0190
9 CR61 1 LIG CAE 2 -0.036 13.0190
10 CB 1 LIG CAF 2 0.141 12.0110
11 N 1 LIG NAG 3 0.000 14.0067
12 H 1 LIG HAA 3 0.000 1.0080
13 CB 1 LIG CAH 4 0.141 12.0110
14 CR61 1 LIG CAI 4 -0.035 13.0190
15 CR61 1 LIG CAK 4 -0.035 13.0190
16 CR61 1 LIG CAM 4 -0.036 13.0190
17 CR61 1 LIG CAL 4 -0.035 13.0190
18 CB 1 LIG CAJ 5 0.000 12.0110
19 CL 1 LIG CLAN 5 0.000 35.4530
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.125 418400.0 0.125 418400.0 ; OAQ CAP
2 3 1 0.125 418400.0 0.125 418400.0 ; CAP OAR
2 4 1 0.153 334720.0 0.153 334720.0 ; CAP CAO
4 5 1 0.153 334720.0 0.153 334720.0 ; CAO CAC
5 6 1 0.139 418400.0 0.139 418400.0 ; CAC CAA
5 10 1 0.139 418400.0 0.139 418400.0 ; CAC CAF
6 7 1 0.139 418400.0 0.139 418400.0 ; CAA CAB
7 8 1 0.139 418400.0 0.139 418400.0 ; CAB CAD
8 9 1 0.139 418400.0 0.139 418400.0 ; CAD CAE
9 10 1 0.139 418400.0 0.139 418400.0 ; CAE CAF
10 11 1 0.133 376560.0 0.133 376560.0 ; CAF NAG
11 12 1 0.100 374468.0 0.100 374468.0 ; NAG HAA
11 13 1 0.133 376560.0 0.133 376560.0 ; NAG CAH
13 14 1 0.139 418400.0 0.139 418400.0 ; CAH CAI
13 18 1 0.139 418400.0 0.139 418400.0 ; CAH CAJ
14 15 1 0.139 418400.0 0.139 418400.0 ; CAI CAK
15 16 1 0.139 418400.0 0.139 418400.0 ; CAK CAM
16 17 1 0.139 418400.0 0.139 418400.0 ; CAM CAL
17 18 1 0.139 418400.0 0.139 418400.0 ; CAL CAJ
18 19 1 0.173 423128.4 0.173 423128.4 ; CAJ CLAN
[ pairs ]
; ai aj fu c0, c1, ...
1 5 1 ; OAQ CAC
2 6 1 ; CAP CAA
2 10 1 ; CAP CAF
3 5 1 ; OAR CAC
4 7 1 ; CAO CAB
4 9 1 ; CAO CAE
4 11 1 ; CAO NAG
5 8 1 ; CAC CAD
5 12 1 ; CAC HAA
5 13 1 ; CAC CAH
6 9 1 ; CAA CAE
6 11 1 ; CAA NAG
7 10 1 ; CAB CAF
8 11 1 ; CAD NAG
9 12 1 ; CAE HAA
9 13 1 ; CAE CAH
10 14 1 ; CAF CAI
10 18 1 ; CAF CAJ
11 15 1 ; NAG CAK
11 17 1 ; NAG CAL
11 19 1 ; NAG CLAN
12 14 1 ; HAA CAI
12 18 1 ; HAA CAJ
13 16 1 ; CAH CAM
14 17 1 ; CAI CAL
14 19 1 ; CAI CLAN
15 18 1 ; CAK CAJ
16 19 1 ; CAM CLAN
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 1 126.0 502.1 126.0 502.1 ; OAQ CAP OAR
1 2 4 1 117.0 502.1 117.0 502.1 ; OAQ CAP CAO
3 2 4 1 117.0 502.1 117.0 502.1 ; OAR CAP CAO
2 4 5 1 109.5 460.2 109.5 460.2 ; CAP CAO CAC
4 5 6 1 120.0 418.4 120.0 418.4 ; CAO CAC CAA
4 5 10 1 126.0 418.4 126.0 418.4 ; CAO CAC CAF
6 5 10 1 120.0 418.4 120.0 418.4 ; CAA CAC CAF
5 6 7 1 120.0 418.4 120.0 418.4 ; CAC CAA CAB
6 7 8 1 120.0 418.4 120.0 418.4 ; CAA CAB CAD
7 8 9 1 120.0 418.4 120.0 418.4 ; CAB CAD CAE
8 9 10 1 120.0 418.4 120.0 418.4 ; CAD CAE CAF
5 10 9 1 120.0 418.4 120.0 418.4 ; CAC CAF CAE
5 10 11 1 120.0 418.4 120.0 418.4 ; CAC CAF NAG
9 10 11 1 120.0 418.4 120.0 418.4 ; CAE CAF NAG
10 11 12 1 120.0 418.4 120.0 418.4 ; CAF NAG HAA
10 11 13 1 120.0 418.4 120.0 418.4 ; CAF NAG CAH
12 11 13 1 120.0 418.4 120.0 418.4 ; HAA NAG CAH
11 13 14 1 120.0 418.4 120.0 418.4 ; NAG CAH CAI
11 13 18 1 120.0 418.4 120.0 418.4 ; NAG CAH CAJ
14 13 18 1 120.0 418.4 120.0 418.4 ; CAI CAH CAJ
13 14 15 1 120.0 418.4 120.0 418.4 ; CAH CAI CAK
14 15 16 1 120.0 418.4 120.0 418.4 ; CAI CAK CAM
15 16 17 1 120.0 418.4 120.0 418.4 ; CAK CAM CAL
16 17 18 1 120.0 418.4 120.0 418.4 ; CAM CAL CAJ
13 18 17 1 120.0 418.4 120.0 418.4 ; CAH CAJ CAL
13 18 19 1 120.0 418.4 120.0 418.4 ; CAH CAJ CLAN
17 18 19 1 120.0 418.4 120.0 418.4 ; CAL CAJ CLAN
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 4 3 1 2 0.0 1673.6 0.0 1673.6 ; imp CAP CAO OAR OAQ
5 10 6 4 2 0.0 1673.6 0.0 1673.6 ; imp CAC CAF CAA CAO
10 5 11 9 2 0.0 1673.6 0.0 1673.6 ; imp CAF CAC NAG CAE
11 10 12 13 2 0.0 1673.6 0.0 1673.6 ; imp NAG CAF HAA CAH
13 11 18 14 2 0.0 1673.6 0.0 1673.6 ; imp CAH NAG CAJ CAI
18 13 19 17 2 0.0 1673.6 0.0 1673.6 ; imp CAJ CAH CLAN CAL
13 14 15 16 2 0.0 1673.6 0.0 1673.6 ; imp CAH CAI CAK CAM
14 15 16 17 2 0.0 1673.6 0.0 1673.6 ; imp CAI CAK CAM CAL
15 16 17 18 2 0.0 1673.6 0.0 1673.6 ; imp CAK CAM CAL CAJ
16 17 18 13 2 0.0 1673.6 0.0 1673.6 ; imp CAM CAL CAJ CAH
17 18 13 14 2 0.0 1673.6 0.0 1673.6 ; imp CAL CAJ CAH CAI
18 13 14 15 2 0.0 1673.6 0.0 1673.6 ; imp CAJ CAH CAI CAK
5 6 7 8 2 0.0 1673.6 0.0 1673.6 ; imp CAC CAA CAB CAD
6 7 8 9 2 0.0 1673.6 0.0 1673.6 ; imp CAA CAB CAD CAE
7 8 9 10 2 0.0 1673.6 0.0 1673.6 ; imp CAB CAD CAE CAF
8 9 10 5 2 0.0 1673.6 0.0 1673.6 ; imp CAD CAE CAF CAC
9 10 5 6 2 0.0 1673.6 0.0 1673.6 ; imp CAE CAF CAC CAA
10 5 6 7 2 0.0 1673.6 0.0 1673.6 ; imp CAF CAC CAA CAB
5 4 2 1 1 0.0 0.4 6 0.0 0.4 6 ; dih CAC CAO CAP OAQ
10 5 4 2 1 0.0 0.4 6 0.0 0.4 6 ; dih CAF CAC CAO CAP
5 10 11 13 1 180.0 33.5 2 180.0 33.5 2 ; dih CAC CAF NAG CAH
10 11 13 18 1 180.0 33.5 2 180.0 33.5 2 ; dih CAF NAG CAH CAJ
sir,your help is most appreciated.
thank you.
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12 years 8 months ago #761
by syahidah
Replied by syahidah on topic newbies in CGMD
sir,i did the antechamber to get the parameter file
however, the output produced is in all-atom format,
may i know how to define the [mapping] part if the structure is in all-atom?
because in tutorial, the parameter file is in united atom format.
your cooperation are much appreciated.
thank you,sir
syahida
however, the output produced is in all-atom format,
may i know how to define the [mapping] part if the structure is in all-atom?
because in tutorial, the parameter file is in united atom format.
your cooperation are much appreciated.
thank you,sir
syahida
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12 years 8 months ago #762
by xavier
Replied by xavier on topic newbies in CGMD
The only difference between all-atom and united-atom are a few Hydrogens. The procedure is basically unchanged. You should just consider the hydrogens as part of the group you are mapping, basically as if they were not there!
Note that the mapping may have different solutions and it is you to try a few possibilities and select the best according to the data (atomistic simulations or experimental data) you have at hand.
Good luck,
XAvier.
Note that the mapping may have different solutions and it is you to try a few possibilities and select the best according to the data (atomistic simulations or experimental data) you have at hand.
Good luck,
XAvier.
syahidah wrote: sir,i did the antechamber to get the parameter file
however, the output produced is in all-atom format,
may i know how to define the [mapping] part if the structure is in all-atom?
because in tutorial, the parameter file is in united atom format.
your cooperation are much appreciated.
thank you,sir
syahida
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12 years 8 months ago #763
by syahidah
Replied by syahidah on topic newbies in CGMD
hi sir,
"The only difference between all-atom and united-atom are a few Hydrogens. The procedure is basically unchanged. You should just consider the hydrogens as part of the group you are mapping, basically as if they were not there!"
did you mean that in the [mapping] section, we just need to put the atom number of carbon or other atom except hydrogen.
let say if we have this;
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB
1 c3 1 DRG CAA 1 -0.09560 12.000000
2 hc 1 DRG HAA 2 0.03483 1.000000
3 hc 1 DRG HAB 3 0.03397 1.000000
4 hc 1 DRG HAC 4 0.03288 1.000000
5 c3 1 DRG CAG 5 -0.09203 12.000000
6 hc 1 DRG HAM 6 0.04579 1.000000
7 hc 1 DRG HAN 7 0.03861 1.000000
8 c3 1 DRG CAH 8 -0.08789 12.000000
9 hc 1 DRG HAO 9 0.04686 1.000000
10 hc 1 DRG HAP 10 0.03960 1.000000
11 c3 1 DRG CAI 11 -0.08771 12.000000
so,is that the [mapping] part need to be done like this?
[mapping]
cg i j k l m
1 1 5 8 11
thank you sir,
syahida
"The only difference between all-atom and united-atom are a few Hydrogens. The procedure is basically unchanged. You should just consider the hydrogens as part of the group you are mapping, basically as if they were not there!"
did you mean that in the [mapping] section, we just need to put the atom number of carbon or other atom except hydrogen.
let say if we have this;
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB
1 c3 1 DRG CAA 1 -0.09560 12.000000
2 hc 1 DRG HAA 2 0.03483 1.000000
3 hc 1 DRG HAB 3 0.03397 1.000000
4 hc 1 DRG HAC 4 0.03288 1.000000
5 c3 1 DRG CAG 5 -0.09203 12.000000
6 hc 1 DRG HAM 6 0.04579 1.000000
7 hc 1 DRG HAN 7 0.03861 1.000000
8 c3 1 DRG CAH 8 -0.08789 12.000000
9 hc 1 DRG HAO 9 0.04686 1.000000
10 hc 1 DRG HAP 10 0.03960 1.000000
11 c3 1 DRG CAI 11 -0.08771 12.000000
so,is that the [mapping] part need to be done like this?
[mapping]
cg i j k l m
1 1 5 8 11
thank you sir,
syahida
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- xavier
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12 years 8 months ago #768
by xavier
Replied by xavier on topic newbies in CGMD
It depends what you intend to do.
For a AT to CG transformation that would be fine.
for a CG to AT transformation all atoms have to be defined obviously.
XAvier.
For a AT to CG transformation that would be fine.
for a CG to AT transformation all atoms have to be defined obviously.
XAvier.
syahidah wrote: hi sir,
"The only difference between all-atom and united-atom are a few Hydrogens. The procedure is basically unchanged. You should just consider the hydrogens as part of the group you are mapping, basically as if they were not there!"
did you mean that in the [mapping] section, we just need to put the atom number of carbon or other atom except hydrogen.
let say if we have this;
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB
1 c3 1 DRG CAA 1 -0.09560 12.000000
2 hc 1 DRG HAA 2 0.03483 1.000000
3 hc 1 DRG HAB 3 0.03397 1.000000
4 hc 1 DRG HAC 4 0.03288 1.000000
5 c3 1 DRG CAG 5 -0.09203 12.000000
6 hc 1 DRG HAM 6 0.04579 1.000000
7 hc 1 DRG HAN 7 0.03861 1.000000
8 c3 1 DRG CAH 8 -0.08789 12.000000
9 hc 1 DRG HAO 9 0.04686 1.000000
10 hc 1 DRG HAP 10 0.03960 1.000000
11 c3 1 DRG CAI 11 -0.08771 12.000000
so,is that the [mapping] part need to be done like this?
[mapping]
cg i j k l m
1 1 5 8 11
thank you sir,
syahida
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