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Using initram.sh
- nanogod
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10 years 8 months ago #1814
by nanogod
Using initram.sh was created by nanogod
Hey guys,
anyone tried the backward (initram.sh) script yet? I supply the following information:
./initram.sh -f 600ns.pdb -p fg.top
and it returns:
Now executing...
./initram.sh -f 600ns.pdb -p fg.top
Checking dependencies:
backward.py ... /home/morten/Dokumenter/600ns/backward.py
grompp ... Missing dependency: grompp
Does anyone know what I did wrong? Also, do I need to supplie a fg itp file for my protein and spc water in the top file? The manual seems abit weak on this :)
Kind regards
Nanogod
anyone tried the backward (initram.sh) script yet? I supply the following information:
./initram.sh -f 600ns.pdb -p fg.top
and it returns:
Now executing...
./initram.sh -f 600ns.pdb -p fg.top
Checking dependencies:
backward.py ... /home/morten/Dokumenter/600ns/backward.py
grompp ... Missing dependency: grompp
Does anyone know what I did wrong? Also, do I need to supplie a fg itp file for my protein and spc water in the top file? The manual seems abit weak on this :)
Kind regards
Nanogod
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- xavier
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10 years 8 months ago #1815
by xavier
Replied by xavier on topic Using initram.sh
This script is quite new and no one at the moment will be able to help.
You'll have to wait the end of the holiday season :))
But please share you experience ....
You'll have to wait the end of the holiday season :))
But please share you experience ....
nanogod wrote: Hey guys,
anyone tried the backward (initram.sh) script yet? I supply the following information:
./initram.sh -f 600ns.pdb -p fg.top
and it returns:
Now executing...
./initram.sh -f 600ns.pdb -p fg.top
Checking dependencies:
backward.py ... /home/morten/Dokumenter/600ns/backward.py
grompp ... Missing dependency: grompp
Does anyone know what I did wrong? Also, do I need to supplie a fg itp file for my protein and spc water in the top file? The manual seems abit weak on this :)
Kind regards
Nanogod
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- djurre
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10 years 8 months ago #1816
by djurre
Replied by djurre on topic Using initram.sh
I'm not sure what is going wrong, but based on the error message I'm guessing you don't have "grompp" in your path. Eg: if you type grompp (or g_luck) on the command line that does not work. If I'm right and there is no grompp, you could do two things:
Open initram.sh and do a search-replace for "grompp" replacing it by "where/ever/grompp/is" (it might also be "grompp_d" in your case).
Or:
Make and alias called "grompp" to "where/ever/grompp/is".
I would choose the second option. If you do have "grompp" in your path, maybe you are using a different shell (not bash) and something goes wrong there.
About the atomistic topology: Yes, you do need a full, complete top file, with all the itp's included. Just as you would get it from "pdb2gmx".
Open initram.sh and do a search-replace for "grompp" replacing it by "where/ever/grompp/is" (it might also be "grompp_d" in your case).
Or:
Make and alias called "grompp" to "where/ever/grompp/is".
I would choose the second option. If you do have "grompp" in your path, maybe you are using a different shell (not bash) and something goes wrong there.
About the atomistic topology: Yes, you do need a full, complete top file, with all the itp's included. Just as you would get it from "pdb2gmx".
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- nanogod
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10 years 8 months ago #1818
by nanogod
Replied by nanogod on topic Using initram.sh
yea djurre you are right, I have version 3.3.3 of gromacs for reverse transformation installed besides 4.6 so I have the suffix _d46. Tried replysing grompp and mdrun with grompp_d46 and mdrun_d46 but a new problem arises :)
Now executing...
./initram.sh -f 600ns.pdb -p fg.top
Checking dependencies:
backward.py ... /home/morten/Dokumenter/600ns/backward.py
f ... Missing dependency: f
I dont have time to look into it right now, but will write later if I figure it out
Now executing...
./initram.sh -f 600ns.pdb -p fg.top
Checking dependencies:
backward.py ... /home/morten/Dokumenter/600ns/backward.py
f ... Missing dependency: f
I dont have time to look into it right now, but will write later if I figure it out
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- tsjerk
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10 years 8 months ago #1819
by tsjerk
Replied by tsjerk on topic Using initram.sh
Hey :)
Probably you made a typo when modifying the script. The variable DEPENDENCIES should list the executable files that are required for running. It seems you put 'f' there.
Cheers,
Tsjerk
Probably you made a typo when modifying the script. The variable DEPENDENCIES should list the executable files that are required for running. It seems you put 'f' there.
Cheers,
Tsjerk
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10 years 8 months ago #1824
by rvanlehn
Replied by rvanlehn on topic Using initram.sh
Hello,
Just did a very quick test of the new script and it worked great. A quick note that stumped me for a little bit - for my initial test, I was trying to do a conversion to the GROMOS 54a7 forcefield which is the default setting for the "-to" input field for initram. This repeatedly failed with the error "Unknown residue: %s..." on residue DPPC, which was clearly present in all topology files and the input CG structure file, and matched with what was in the dppc.gromos.map file. However, changing the "-to" field to just "gromos" worked fine, i.e.:
./initram -f dppc_bilayer.gro -p atomistic_topol.top -to gromos
I thought maybe this is because the default mapping files all are of the form *.gromos.map? Not sure whether this was an error on my side or something I'm not realizing from the help documentation.
Thanks for this tool!
Reid
Just did a very quick test of the new script and it worked great. A quick note that stumped me for a little bit - for my initial test, I was trying to do a conversion to the GROMOS 54a7 forcefield which is the default setting for the "-to" input field for initram. This repeatedly failed with the error "Unknown residue: %s..." on residue DPPC, which was clearly present in all topology files and the input CG structure file, and matched with what was in the dppc.gromos.map file. However, changing the "-to" field to just "gromos" worked fine, i.e.:
./initram -f dppc_bilayer.gro -p atomistic_topol.top -to gromos
I thought maybe this is because the default mapping files all are of the form *.gromos.map? Not sure whether this was an error on my side or something I'm not realizing from the help documentation.
Thanks for this tool!
Reid
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- tsjerk
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10 years 8 months ago #1825
by tsjerk
Replied by tsjerk on topic Using initram.sh
Hey :)
I'm glad you like the program.
It should be possible to specify the version of gromos, like gromos54a7. This does not depend on the file name, but on the force field listed in the mapping file, under [ mapping ]. Maybe I overlooked DPPC. I'll see that it gets fixed. In case you're interested, the manuscript has been submitted. I'll put a reference on the site as soon as it's through.
Cheers,
Tsjerk
I'm glad you like the program.
It should be possible to specify the version of gromos, like gromos54a7. This does not depend on the file name, but on the force field listed in the mapping file, under [ mapping ]. Maybe I overlooked DPPC. I'll see that it gets fixed. In case you're interested, the manuscript has been submitted. I'll put a reference on the site as soon as it's through.
Cheers,
Tsjerk
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- rvanlehn
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10 years 8 months ago #1826
by rvanlehn
Replied by rvanlehn on topic Using initram.sh
Ah OK, I see where it is specified - the default mapping is indeed "gromos" hence the error. The mapping file looks pretty straightforward so I should be able to change that as needed. Since the mapping is based off of atom names and not types I don't think there would be any difference between different versions of GROMOS anyway (although I've exclusively worked with 54a7).
Anyway, I'll look for the paper when it's out and thanks for the help!
Reid
Anyway, I'll look for the paper when it's out and thanks for the help!
Reid
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- tsjerk
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10 years 8 months ago #1827
by tsjerk
Replied by tsjerk on topic Using initram.sh
Hi Reid,
Between GROMOS versions, the aromatic rings may differ, bearing no hydrogens in the earlier versions. For the rest there are no differences in terms of atom names and order.
Cheers,
Tsjerk
Between GROMOS versions, the aromatic rings may differ, bearing no hydrogens in the earlier versions. For the rest there are no differences in terms of atom names and order.
Cheers,
Tsjerk
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- nanogod
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10 years 7 months ago #1996
by nanogod
Replied by nanogod on topic Using initram.sh
I have been using the script quite a lot and I am pretty happy with how it performece. Mainly compared with the olde script for gromacs 3.3! I have two things though:
1.: I see that mapping for amber is found in the mapping folder but not optional in the script. I have manually added this by adding "amber": 0, in the force filed lelvel list and it seems to be working. My question is hence directed at any bugs associated with converting to amber as it was not fully included or integrated into the script?
2.: I notice that the converted FG structure varies a lote even for the same structure. For instance I see that some peptides assume a different secondary structure after a convetion, even though I use exacly the same files and parameteres. I there a way this "randomness" might be reduced, forinstance by increasing the minimizatioin step?
Kind regards
Nanogod
1.: I see that mapping for amber is found in the mapping folder but not optional in the script. I have manually added this by adding "amber": 0, in the force filed lelvel list and it seems to be working. My question is hence directed at any bugs associated with converting to amber as it was not fully included or integrated into the script?
2.: I notice that the converted FG structure varies a lote even for the same structure. For instance I see that some peptides assume a different secondary structure after a convetion, even though I use exacly the same files and parameteres. I there a way this "randomness" might be reduced, forinstance by increasing the minimizatioin step?
Kind regards
Nanogod
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- nanogod
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10 years 7 months ago - 10 years 7 months ago #1997
by nanogod
Replied by nanogod on topic Using initram.sh
Ohh and another thing :) When I construct my fg top file for the script I get a bug if I include SOL and the amount. Insted I list only my protein amount, however in the end the script acounts for the SOL and writes the correct number in the produced top file.
Let me know if you understand what I mean to say :)
Let me know if you understand what I mean to say :)
Last edit: 10 years 7 months ago by nanogod.
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10 years 1 month ago #3593
by nw79
Replied by nw79 on topic Using initram.sh
Hi,
I am trying to define a mapping scheme for DPPG in gromos (specifically gromos53a6) to use the backward tool for a membrane containing DPPG and DPPC. This is the mapping scheme I came up with:
;Created on 13.03.2014
[ molecule ]
DPPG
[ martini ]
GLH PO4 GL1 GL2 C1A C2A C3A C4A C1B C2B C3B C4B
;
;GLH-PO4-GL1-C1A-C2A-C3A-C4A
; |
; GL2-C1B-C2B-C3B-C4B
[ mapping ]
gromos
[ atoms ]
; Terminal head group (glycerol)
1 H0 GLH
2 01 GLH
3 C2 GLH
4 C3 GLH GLH GLH PO4
5 O4 GLH
6 H5 GLH
7 C6 GLH PO4
;Phosphate group
8 O7 PO4 PO4 GLH
9 P8 PO4
10 O9 PO4
11 O10 PO4
12 O11 PO4 PO4 GL1
;Diacylglycerol
12 CC GL1 GL1 PO4
13 CD GL1
14 OE GL1 GL1 GL1 C1A
15 C1A GL1 C1A
16 OF
17 C1B C1A C1A C1A GL1
18 C1C C1A
19 C1D C1A C1A C2A
20 C1E C1A C2A
21 C1F C2A C2A C1A
22 C1G C2A
23 C1H C2A C2A C3A
24 C1I C2A C3A
25 C1J C3A C3A C2A
26 C1K C3A
27 C1L C3A C3A C4A
28 C1M C3A C4A
29 C1N C4A C4A C3A
30 C1O C4A C4A C4A C3A
31 C1P C4A
32 CE GL2
33 OG GL2 GL2 GL2 C1B
34 C2A GL2 C1B
35 OH
36 C2B C1B C1B C1B GL2
37 C2C C1B
38 C2D C1B C1B C2B
39 C2E C1B C2B
40 C2F C2B C2B C1B
41 C2G C2B
42 C2H C2B C2B C3B
43 C2I C2B C3B
44 C2J C3B C3B C2B
45 C2K C3B
46 C2L C3B C3B C4B
47 C2M C3B C4B
48 C2N C4B C4B C3B
49 C2O C4B C4B C4B C3B
50 C2P C4B
;;;making a glycerol group
[trans]
H0 O1 C2 C3
[out]
O4 C3 H0 C6
; Acyl esters
; ===========
; This reconstruction is somewhat complex. Unfortunately
; the Gromos united atom force field does not have
; correct dihedrals for acyl esters and these groups
; have to be built with correct geometry. Only setting
; the C-O-CO-C dihedrals correct is not sufficient, as
; the distortions may be so large that the dihedrals
; are pushed over the barrier. Therefore, the whole
; glycerol group is rebuilt so as to form a buffer.
; Acyl ester 1
;
[ chiral ]
x CD OE CE CC
[ trans ]
OF C1A CD x
[ out ]
OE C1A OF C1B
[ trans ]
C1B C1A OE CD
[ out ]
OF C1A OE C1B
; Acyl ester 2
;
[ out ]
y CE CD OG
[ chiral ]
z CE OG CD y
[ trans ]
OH C2A CE z
[ out ]
OG C2A OH C2B
[ trans ]
C2B C2A OG CE
[ out ]
OH C2A OG C2B
When I try to run the script using:
./initram.sh -f cg-system.gro -p system_gromos.top -to gromos
It returns this error:
[('OH', None), ('C2A', None), ('CE', None), ('z', None)]
Not all positions defined for [trans] operation:
[('C2B', None), ('C2A', None), ('OG', None), ('CE', None)]
Not all positions defined for [trans] operation:
[('OF', None), ('C1A', None), ('CD', None), ('x', None)]
Not all positions defined for [trans] operation:
[('C1B', None), ('C1A', None), ('OE', None), ('CD', None)]
Not all positions defined for [trans] operation:
[('OH', None), ('C2A', None), ('CE', None), ('z', None)]
Not all positions defined for [trans] operation:
[('C2B', None), ('C2A', None), ('OG', None), ('CE', None)]
for what seems like all the atoms in the dppg molecules. As there is no gromos mapping scheme for any molecules containing glycerol, I am unsure how to define the trans operations.. (considering that the diacylgycerol chains should be the same as those defined in dppc.gromos.map?)
Any suggestions?
Thanks
I am trying to define a mapping scheme for DPPG in gromos (specifically gromos53a6) to use the backward tool for a membrane containing DPPG and DPPC. This is the mapping scheme I came up with:
;Created on 13.03.2014
[ molecule ]
DPPG
[ martini ]
GLH PO4 GL1 GL2 C1A C2A C3A C4A C1B C2B C3B C4B
;
;GLH-PO4-GL1-C1A-C2A-C3A-C4A
; |
; GL2-C1B-C2B-C3B-C4B
[ mapping ]
gromos
[ atoms ]
; Terminal head group (glycerol)
1 H0 GLH
2 01 GLH
3 C2 GLH
4 C3 GLH GLH GLH PO4
5 O4 GLH
6 H5 GLH
7 C6 GLH PO4
;Phosphate group
8 O7 PO4 PO4 GLH
9 P8 PO4
10 O9 PO4
11 O10 PO4
12 O11 PO4 PO4 GL1
;Diacylglycerol
12 CC GL1 GL1 PO4
13 CD GL1
14 OE GL1 GL1 GL1 C1A
15 C1A GL1 C1A
16 OF
17 C1B C1A C1A C1A GL1
18 C1C C1A
19 C1D C1A C1A C2A
20 C1E C1A C2A
21 C1F C2A C2A C1A
22 C1G C2A
23 C1H C2A C2A C3A
24 C1I C2A C3A
25 C1J C3A C3A C2A
26 C1K C3A
27 C1L C3A C3A C4A
28 C1M C3A C4A
29 C1N C4A C4A C3A
30 C1O C4A C4A C4A C3A
31 C1P C4A
32 CE GL2
33 OG GL2 GL2 GL2 C1B
34 C2A GL2 C1B
35 OH
36 C2B C1B C1B C1B GL2
37 C2C C1B
38 C2D C1B C1B C2B
39 C2E C1B C2B
40 C2F C2B C2B C1B
41 C2G C2B
42 C2H C2B C2B C3B
43 C2I C2B C3B
44 C2J C3B C3B C2B
45 C2K C3B
46 C2L C3B C3B C4B
47 C2M C3B C4B
48 C2N C4B C4B C3B
49 C2O C4B C4B C4B C3B
50 C2P C4B
;;;making a glycerol group
[trans]
H0 O1 C2 C3
[out]
O4 C3 H0 C6
; Acyl esters
; ===========
; This reconstruction is somewhat complex. Unfortunately
; the Gromos united atom force field does not have
; correct dihedrals for acyl esters and these groups
; have to be built with correct geometry. Only setting
; the C-O-CO-C dihedrals correct is not sufficient, as
; the distortions may be so large that the dihedrals
; are pushed over the barrier. Therefore, the whole
; glycerol group is rebuilt so as to form a buffer.
; Acyl ester 1
;
[ chiral ]
x CD OE CE CC
[ trans ]
OF C1A CD x
[ out ]
OE C1A OF C1B
[ trans ]
C1B C1A OE CD
[ out ]
OF C1A OE C1B
; Acyl ester 2
;
[ out ]
y CE CD OG
[ chiral ]
z CE OG CD y
[ trans ]
OH C2A CE z
[ out ]
OG C2A OH C2B
[ trans ]
C2B C2A OG CE
[ out ]
OH C2A OG C2B
When I try to run the script using:
./initram.sh -f cg-system.gro -p system_gromos.top -to gromos
It returns this error:
[('OH', None), ('C2A', None), ('CE', None), ('z', None)]
Not all positions defined for [trans] operation:
[('C2B', None), ('C2A', None), ('OG', None), ('CE', None)]
Not all positions defined for [trans] operation:
[('OF', None), ('C1A', None), ('CD', None), ('x', None)]
Not all positions defined for [trans] operation:
[('C1B', None), ('C1A', None), ('OE', None), ('CD', None)]
Not all positions defined for [trans] operation:
[('OH', None), ('C2A', None), ('CE', None), ('z', None)]
Not all positions defined for [trans] operation:
[('C2B', None), ('C2A', None), ('OG', None), ('CE', None)]
for what seems like all the atoms in the dppg molecules. As there is no gromos mapping scheme for any molecules containing glycerol, I am unsure how to define the trans operations.. (considering that the diacylgycerol chains should be the same as those defined in dppc.gromos.map?)
Any suggestions?
Thanks
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- nw79
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10 years 1 month ago #3595
by nw79
Replied by nw79 on topic Using initram.sh
Hi,
Following on from my previous post, it seems this error comes up even when using lipids that already have a defined mapping scheme. It seems that the program is not recognising gromos lipids, as I do not have this issue when using charmm36.
Is there possibly a discrepancy between the naming scheme used for the mapping files e.g popc.gromos.map relative to those defined by the forcefields topology (itp) files?
For example, looking into the gromos 53a6 published forcefield for running with gromacs (J. Comput. Chem. 2004 vol. 25 (13): 1656-1676), popc lipids atoms are numbered as:
C1
C2
C3
N4... etc
whereas in the mapping file popc.gromos.itp, the atoms are defined as:
CN1
CN2
CN3
NTM
So, when using the aquaporin tutorial example published in the supplementary material of the "Going backward: A flexible geometric approach to reverse transformation from coarse grained to atomistic models" paper, the initram.sh script returns an error:
Fatal error:
number of coordinates in coordinate file (0-backward.gro, 47523)
does not match topology (backmapped.top, 60367)
visualing 0-backmapped.gro, it appears the porin has been recognised, but the lipids are missing.
Could the different numbering schemes defined in the UA topology file (gromos53a6.ff/forcefield.itp) and the dopc.gromos.map file be a source of that error?
Thanks
Following on from my previous post, it seems this error comes up even when using lipids that already have a defined mapping scheme. It seems that the program is not recognising gromos lipids, as I do not have this issue when using charmm36.
Is there possibly a discrepancy between the naming scheme used for the mapping files e.g popc.gromos.map relative to those defined by the forcefields topology (itp) files?
For example, looking into the gromos 53a6 published forcefield for running with gromacs (J. Comput. Chem. 2004 vol. 25 (13): 1656-1676), popc lipids atoms are numbered as:
C1
C2
C3
N4... etc
whereas in the mapping file popc.gromos.itp, the atoms are defined as:
CN1
CN2
CN3
NTM
So, when using the aquaporin tutorial example published in the supplementary material of the "Going backward: A flexible geometric approach to reverse transformation from coarse grained to atomistic models" paper, the initram.sh script returns an error:
Fatal error:
number of coordinates in coordinate file (0-backward.gro, 47523)
does not match topology (backmapped.top, 60367)
visualing 0-backmapped.gro, it appears the porin has been recognised, but the lipids are missing.
Could the different numbering schemes defined in the UA topology file (gromos53a6.ff/forcefield.itp) and the dopc.gromos.map file be a source of that error?
Thanks
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