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normal Warning: atom names in .top and .pdb do not match

  • Kargar
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13 years 2 months ago #524 by Kargar
Warning: atom names in .top and .pdb do not match was created by Kargar
Dear All

I am learning the CG Martini force filed using the tutorial "protein in water" for protein ubiquitin. so I did the things like below:

1. awk -f atom2cg_v2.1.awk 1UBQ.pdb > 1UBQ-cg.pdb (it makes a CG .pdb file)

2. wget ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt

3. grep -A 1 1ubq pdb_seqres.txt > 1ubq.seq (these 2 and 3 commands make a .seq file)

4. ./seq2itp.pl 1ubq.seq 1ubq.ssd > 1ubq.itp (by the use of .seq and .ssd file and seq2itp.pl script I can make a .itp file. I should mention that I used .ssd file prepared by matini group in this tutorial.)

5. I make a 1ubq.top file like below

#include "martini_v2.1.itp"
#include "1ubq.itp"

[ system ]
; name
protein

[ molecules ]
; name number
protein 1

6. grompp -f 1ubq.mdp -c 1UBQ-cg.pdb -p 1ubq.top

but warnings come like this

Warning: atom name 1 in 1ubq.top and 1UBQ-cg.pdb does not match (BBc - BB)
Warning: atom name 2 in 1ubq.top and 1UBQ-cg.pdb does not match (S1c - S1)
Warning: atom name 3 in 1ubq.top and 1UBQ-cg.pdb does not match (BBe - BB)
............

............

all of my atom names mismatch. I checked the 1ubq.itp. some lines are in below

;;; MARTINI 2.1 coarse-grained topology
;;; Generated by seq2itp.pl version 1.1.4

;;; SEQ: MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL 50
;;; SEQ: EDGRTLSDYN IQKESTLHLV LRLRGG
;;; Total Number of Amino Acid Residues: 76


[moleculetype]
;molname exclusions
Protein 1

[atoms]
1 Qd 1 MET BBc 1 1.000 ; COI
2 C5 1 MET S1c 2 0.000 ; COI
3 Nda 2 GLN BBe 3 0.000 ; EXT

........

........

[ bonds ]
;backbone-backbone bonds
1 3 1 0.350 400 ; COI-EXT
3 5 1 0.350 1250 ; EXT-EXT
5 7 1 0.350 1250 ; EXT-EXT

........

........

[ constraints ]
;sc-sc constraints (Ring Structures)
8 9 1 0.270 ; PHE4
8 10 1 0.270 ; PHE4
9 10 1 0.270 ; PHE4

.........

.........

[angles]
;backbone-backbone-backbone angles
1 3 5 2 127.00 25 ; COI-EXT-EXT
3 5 7 2 134.00 25 ; EXT-EXT-EXT
5 7 11 2 134.00 25 ; EXT-EXT-EXT

.............

.............

[dihedrals]
;improper dihedral angles
7 9 10 8 2 0.00 50 ; PHE4
94 96 97 95 2 0.00 50 ; PHE45

..........

..........

I found that for example the word "c" in atom name "BBc" comes from "COI" means coil. so I added manually such these words to my 1UBQ-cg.pdb file acording to 1ubq.itp file. but then again the same warnings. Please help me with these too many warnings.

7. I used -maxwarn, but when I used the command "mdrun" the message like this appears:

Back Off! I just backed up md.log to ./#md.log.3#
Getting Loaded...
Reading file topol.tpr, VERSION 4.0.7 (single precision)
Loaded with Money


Back Off! I just backed up traj.trr to ./#traj.trr.1#

Back Off! I just backed up traj.xtc to ./#traj.xtc.1#

Back Off! I just backed up ener.edr to ./#ener.edr.1#
starting mdrun 'protein'
5000 steps, 200.0 ps.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.063064, max 0.267666 (between atoms 46 and 47)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
145 146 47.6 0.2741 0.2693 0.2700
146 147 35.9 0.2740 0.2662 0.2700
46 47 103.9 0.2600 0.3296 0.2600
92 93 48.3 0.3100 0.3100 0.3100
115 116 101.4 0.2600 0.3164 0.2600
step 0
Step 1, time 0.04 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 241.839513, max 1323.171997 (between atoms 115 and 116)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
145 146 42.0 0.2693 0.2674 0.2700
145 147 31.4 0.2759 0.2727 0.2700
46 47 90.9 0.3296 16.2862 0.2600
48 49 106.0 0.3100 1.1217 0.3100
92 93 48.1 0.3100 0.3100 0.3100
115 116 90.0 0.3164 344.2847 0.2600

Back Off! I just backed up step1b.pdb to ./#step1b.pdb.1#

Back Off! I just backed up step1c.pdb to ./#step1c.pdb.1#
Wrote pdb files with previous and current coordinates
Segmentation fault

Does this error relate to too many warnings of atom names mismatching?

I changed the lincs_warnangle to 90 degrees but the same massage appeared.

Thank you in advance

Kargar

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13 years 2 months ago #529 by xavier
Replied by xavier on topic Warning: atom names in .top and .pdb do not match
Dear Kargar,

it is indeed necessary to use the maxwarn option in the grompp command as the name mismatch is expected. You made a good choice.

The second problem you face in the mdrun ... lincs warnings ... is often a indication that the starting structure is not optimal, so that he constrains can not be fulfilled. One solution is to turn off all constraints and replace them by bonds with a large force constant (20000 kJ/mol/nm^2).

Kargar wrote: Dear All

I am learning the CG Martini force filed using the tutorial "protein in water" for protein ubiquitin. so I did the things like below:

1. awk -f atom2cg_v2.1.awk 1UBQ.pdb > 1UBQ-cg.pdb (it makes a CG .pdb file)

2. wget ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt

3. grep -A 1 1ubq pdb_seqres.txt > 1ubq.seq (these 2 and 3 commands make a .seq file)

4. ./seq2itp.pl 1ubq.seq 1ubq.ssd > 1ubq.itp (by the use of .seq and .ssd file and seq2itp.pl script I can make a .itp file. I should mention that I used .ssd file prepared by matini group in this tutorial.)

5. I make a 1ubq.top file like below

#include "martini_v2.1.itp"
#include "1ubq.itp"

[ system ]
; name
protein

[ molecules ]
; name number
protein 1

6. grompp -f 1ubq.mdp -c 1UBQ-cg.pdb -p 1ubq.top

but warnings come like this

Warning: atom name 1 in 1ubq.top and 1UBQ-cg.pdb does not match (BBc - BB)
Warning: atom name 2 in 1ubq.top and 1UBQ-cg.pdb does not match (S1c - S1)
Warning: atom name 3 in 1ubq.top and 1UBQ-cg.pdb does not match (BBe - BB)
............

............

all of my atom names mismatch. I checked the 1ubq.itp. some lines are in below

;;; MARTINI 2.1 coarse-grained topology
;;; Generated by seq2itp.pl version 1.1.4

;;; SEQ: MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL 50
;;; SEQ: EDGRTLSDYN IQKESTLHLV LRLRGG
;;; Total Number of Amino Acid Residues: 76


[moleculetype]
;molname exclusions
Protein 1

[atoms]
1 Qd 1 MET BBc 1 1.000 ; COI
2 C5 1 MET S1c 2 0.000 ; COI
3 Nda 2 GLN BBe 3 0.000 ; EXT

........

........

[ bonds ]
;backbone-backbone bonds
1 3 1 0.350 400 ; COI-EXT
3 5 1 0.350 1250 ; EXT-EXT
5 7 1 0.350 1250 ; EXT-EXT

........

........

[ constraints ]
;sc-sc constraints (Ring Structures)
8 9 1 0.270 ; PHE4
8 10 1 0.270 ; PHE4
9 10 1 0.270 ; PHE4

.........

.........

[angles]
;backbone-backbone-backbone angles
1 3 5 2 127.00 25 ; COI-EXT-EXT
3 5 7 2 134.00 25 ; EXT-EXT-EXT
5 7 11 2 134.00 25 ; EXT-EXT-EXT

.............

.............

[dihedrals]
;improper dihedral angles
7 9 10 8 2 0.00 50 ; PHE4
94 96 97 95 2 0.00 50 ; PHE45

..........

..........

I found that for example the word "c" in atom name "BBc" comes from "COI" means coil. so I added manually such these words to my 1UBQ-cg.pdb file acording to 1ubq.itp file. but then again the same warnings. Please help me with these too many warnings.

7. I used -maxwarn, but when I used the command "mdrun" the message like this appears:

Back Off! I just backed up md.log to ./#md.log.3#
Getting Loaded...
Reading file topol.tpr, VERSION 4.0.7 (single precision)
Loaded with Money


Back Off! I just backed up traj.trr to ./#traj.trr.1#

Back Off! I just backed up traj.xtc to ./#traj.xtc.1#

Back Off! I just backed up ener.edr to ./#ener.edr.1#
starting mdrun 'protein'
5000 steps, 200.0 ps.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.063064, max 0.267666 (between atoms 46 and 47)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
145 146 47.6 0.2741 0.2693 0.2700
146 147 35.9 0.2740 0.2662 0.2700
46 47 103.9 0.2600 0.3296 0.2600
92 93 48.3 0.3100 0.3100 0.3100
115 116 101.4 0.2600 0.3164 0.2600
step 0
Step 1, time 0.04 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 241.839513, max 1323.171997 (between atoms 115 and 116)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
145 146 42.0 0.2693 0.2674 0.2700
145 147 31.4 0.2759 0.2727 0.2700
46 47 90.9 0.3296 16.2862 0.2600
48 49 106.0 0.3100 1.1217 0.3100
92 93 48.1 0.3100 0.3100 0.3100
115 116 90.0 0.3164 344.2847 0.2600

Back Off! I just backed up step1b.pdb to ./#step1b.pdb.1#

Back Off! I just backed up step1c.pdb to ./#step1c.pdb.1#
Wrote pdb files with previous and current coordinates
Segmentation fault

Does this error relate to too many warnings of atom names mismatching?

I changed the lincs_warnangle to 90 degrees but the same massage appeared.

Thank you in advance

Kargar

Please Log in or Create an account to join the conversation.

  • Kargar
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13 years 2 months ago #554 by Kargar
Replied by Kargar on topic Warning: atom names in .top and .pdb do not match
Dear Martini Team
Thank you very much for your reply. as you mentioned I should turn off all constraints and replace them by bonds with a large force constant (20000 kJ/mol/nm^2). I study the .mdp file but I could not find anywhere to change the force constant. one of the input files for mdrun is topol.tpr that contains the molecular topology and all the simulation parameters. so do you mean I should change all of the force constants in the topology file or 1ubq.itp file manually?please guide me.
For turning off the constraints, in the .mdp file I choose "none" for constraints. But when I run the simulation then again the same errors with "Lincs" appeare?!? I expected all constraints to be off!?! please help me.
Thank you
Kargar

xavier wrote: Dear Kargar,

it is indeed necessary to use the maxwarn option in the grompp command as the name mismatch is expected. You made a good choice.

The second problem you face in the mdrun ... lincs warnings ... is often a indication that the starting structure is not optimal, so that he constrains can not be fulfilled. One solution is to turn off all constraints and replace them by bonds with a large force constant (20000 kJ/mol/nm^2).

Kargar wrote: Dear All

I am learning the CG Martini force filed using the tutorial "protein in water" for protein ubiquitin. so I did the things like below:

1. awk -f atom2cg_v2.1.awk 1UBQ.pdb > 1UBQ-cg.pdb (it makes a CG .pdb file)

2. wget ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt

3. grep -A 1 1ubq pdb_seqres.txt > 1ubq.seq (these 2 and 3 commands make a .seq file)

4. ./seq2itp.pl 1ubq.seq 1ubq.ssd > 1ubq.itp (by the use of .seq and .ssd file and seq2itp.pl script I can make a .itp file. I should mention that I used .ssd file prepared by matini group in this tutorial.)

5. I make a 1ubq.top file like below

#include "martini_v2.1.itp"
#include "1ubq.itp"

[ system ]
; name
protein

[ molecules ]
; name number
protein 1

6. grompp -f 1ubq.mdp -c 1UBQ-cg.pdb -p 1ubq.top

but warnings come like this

Warning: atom name 1 in 1ubq.top and 1UBQ-cg.pdb does not match (BBc - BB)
Warning: atom name 2 in 1ubq.top and 1UBQ-cg.pdb does not match (S1c - S1)
Warning: atom name 3 in 1ubq.top and 1UBQ-cg.pdb does not match (BBe - BB)
............

............

all of my atom names mismatch. I checked the 1ubq.itp. some lines are in below

;;; MARTINI 2.1 coarse-grained topology
;;; Generated by seq2itp.pl version 1.1.4

;;; SEQ: MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL 50
;;; SEQ: EDGRTLSDYN IQKESTLHLV LRLRGG
;;; Total Number of Amino Acid Residues: 76


[moleculetype]
;molname exclusions
Protein 1

[atoms]
1 Qd 1 MET BBc 1 1.000 ; COI
2 C5 1 MET S1c 2 0.000 ; COI
3 Nda 2 GLN BBe 3 0.000 ; EXT

........

........

[ bonds ]
;backbone-backbone bonds
1 3 1 0.350 400 ; COI-EXT
3 5 1 0.350 1250 ; EXT-EXT
5 7 1 0.350 1250 ; EXT-EXT

........

........

[ constraints ]
;sc-sc constraints (Ring Structures)
8 9 1 0.270 ; PHE4
8 10 1 0.270 ; PHE4
9 10 1 0.270 ; PHE4

.........

.........

[angles]
;backbone-backbone-backbone angles
1 3 5 2 127.00 25 ; COI-EXT-EXT
3 5 7 2 134.00 25 ; EXT-EXT-EXT
5 7 11 2 134.00 25 ; EXT-EXT-EXT

.............

.............

[dihedrals]
;improper dihedral angles
7 9 10 8 2 0.00 50 ; PHE4
94 96 97 95 2 0.00 50 ; PHE45

..........

..........

I found that for example the word "c" in atom name "BBc" comes from "COI" means coil. so I added manually such these words to my 1UBQ-cg.pdb file acording to 1ubq.itp file. but then again the same warnings. Please help me with these too many warnings.

7. I used -maxwarn, but when I used the command "mdrun" the message like this appears:

Back Off! I just backed up md.log to ./#md.log.3#
Getting Loaded...
Reading file topol.tpr, VERSION 4.0.7 (single precision)
Loaded with Money


Back Off! I just backed up traj.trr to ./#traj.trr.1#

Back Off! I just backed up traj.xtc to ./#traj.xtc.1#

Back Off! I just backed up ener.edr to ./#ener.edr.1#
starting mdrun 'protein'
5000 steps, 200.0 ps.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.063064, max 0.267666 (between atoms 46 and 47)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
145 146 47.6 0.2741 0.2693 0.2700
146 147 35.9 0.2740 0.2662 0.2700
46 47 103.9 0.2600 0.3296 0.2600
92 93 48.3 0.3100 0.3100 0.3100
115 116 101.4 0.2600 0.3164 0.2600
step 0
Step 1, time 0.04 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 241.839513, max 1323.171997 (between atoms 115 and 116)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
145 146 42.0 0.2693 0.2674 0.2700
145 147 31.4 0.2759 0.2727 0.2700
46 47 90.9 0.3296 16.2862 0.2600
48 49 106.0 0.3100 1.1217 0.3100
92 93 48.1 0.3100 0.3100 0.3100
115 116 90.0 0.3164 344.2847 0.2600

Back Off! I just backed up step1b.pdb to ./#step1b.pdb.1#

Back Off! I just backed up step1c.pdb to ./#step1c.pdb.1#
Wrote pdb files with previous and current coordinates
Segmentation fault

Does this error relate to too many warnings of atom names mismatching?

I changed the lincs_warnangle to 90 degrees but the same massage appeared.

Thank you in advance

Kargar

Please Log in or Create an account to join the conversation.

More
13 years 2 months ago #566 by xavier
Replied by xavier on topic Warning: atom names in .top and .pdb do not match

Kargar wrote: Dear Martini Team
Thank you very much for your reply. as you mentioned I should turn off all constraints and replace them by bonds with a large force constant (20000 kJ/mol/nm^2). I study the .mdp file but I could not find anywhere to change the force constant. one of the input files for mdrun is topol.tpr that contains the molecular topology and all the simulation parameters. so do you mean I should change all of the force constants in the topology file or 1ubq.itp file manually?please guide me.

Yes, unfortunately you have to make the changes in the topology by hand. It is not so complicated :))

For turning off the constraints, in the .mdp file I choose "none" for constraints. But when I run the simulation then again the same errors with "Lincs" appeare?!? I expected all constraints to be off!?! please help me.

The constrains defined in the topology are not affected by the "constrains" keyword in the the mdp file. It is used to automatically turn certain bonds (all-bonds, H-bonds, ...) into constrains.

Thank you
Kargar

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12 years 10 months ago #727 by Melchor
Replied by Melchor on topic Warning: atom names in .top and .pdb do not match
Hi,

I am trying to carry out the "Protein in Water" tutorial, and I have the same problem that ypu are discussing in this topic. I am doing the same but with water in the media.

I turn-off the constrainst in the mdp file and I convert the constraints of itp file into bonds with a force constant of 20000 KJ/mol/nm^2.

I do it like this:

;sc-sc constraints (Ring Structures)
8 9 1 0.270 20000 ; PHE4
8 10 1 0.270 20000 ; PHE4
9 10 1 0.270 20000 ; PHE4

....
....
.....

;bc-sc constraints (ITV)
5 6 1 0.310 20000 ; ILE3
11 12 1 0.265 20000 ; VAL5
16 17 1 0.260 20000 ; THR7
20 21 1 0.260 20000 ; THR9
26 27 1 0.260 20000 ; THR12
28 29 1 0.310 20000 ; ILE13
30 31 1 0.260 20000 ; THR14
36 37 1 0.265 20000 ; VAL17
46 47 1 0.260 20000 ; THR22
48 49 1 0.310 20000 ; ILE23

....
...
....

When I try to run mdrun for equilibrate the solvent or for the whole protein without equilibrate the solvent before,

mdrun -f example.mdp -c md1.pdb -g md1.log &


I obtain a segmentation fault as result.

For 20 ps

Back Off! I just backed up md1.log to ./#md1.log.4#
Reading file topol.tpr, VERSION 4.0.7 (single precision)

Back Off! I just backed up traj.trr to ./#traj.trr.7#

Back Off! I just backed up traj.xtc to ./#traj.xtc.7#

Back Off! I just backed up ener.edr to ./#ener.edr.7#
starting mdrun 'protein in water'
10000 steps, 20.0 ps.

Step 1 Warning: pressure scaling more than 1%, mu: 20.6639 20.6639 28.1722

[1]+ Segmentation fault mdrun -f example.mdp -c md1.pdb -g md1.log


For 200 ps

Back Off! I just backed up md1.log to ./#md1.log.5#
Reading file topol.tpr, VERSION 4.0.7 (single precision)

Back Off! I just backed up traj.trr to ./#traj.trr.8#

Back Off! I just backed up traj.xtc to ./#traj.xtc.8#

Back Off! I just backed up ener.edr to ./#ener.edr.8#
starting mdrun 'protein in water'
10000 steps, 200.0 ps.

[1]+ Segmentation fault mdrun -f example2.mdp -c md1.pdb -g md1.log
melchor@blauet:~/CSIC/calculos/Martini/Prueba$

My mdp file is like this:

title = Martini tutorial protein in water
cpp = /usr/bin/cpp

integrator = md
tinit = 0.0
dt = 0.02
nsteps = 10000
nstcomm = 1
comm-grps =

nstxout = 10000
nstvout = 10000
nstfout = 0
nstlog = 10000
nstenergy = 10000
nstxtcout = 1000
xtc_precision = 100
xtc-grps =
energygrps = protein W
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2

coulombtype = PME ; SHIFT
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 2.5
vdw_type = shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = protein W
tau_t = 0.1 0.1
ref_t = 320 320
Pcoupl = berendsen
Pcoupltype = semiisotropic
tau_p = 1.0 1.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0

gen_vel = no
gen_temp = 320
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30


I have revised forums at internet,web pages, Gromacs manual, etc and I don't know what can I do. If you can suggest me a form of solve my problem I will be very pleasure.

Grettings,

Melchor S.

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12 years 10 months ago #728 by xavier
Replied by xavier on topic Warning: atom names in .top and .pdb do not match
I think that the first thing you want to do is to minimize the system. That should fix all your problems.

XAvier.

Melchor wrote: Hi,

I am trying to carry out the "Protein in Water" tutorial, and I have the same problem that ypu are discussing in this topic. I am doing the same but with water in the media.

I turn-off the constrainst in the mdp file and I convert the constraints of itp file into bonds with a force constant of 20000 KJ/mol/nm^2.

I do it like this:

;sc-sc constraints (Ring Structures)
8 9 1 0.270 20000 ; PHE4
8 10 1 0.270 20000 ; PHE4
9 10 1 0.270 20000 ; PHE4

....
....
.....

;bc-sc constraints (ITV)
5 6 1 0.310 20000 ; ILE3
11 12 1 0.265 20000 ; VAL5
16 17 1 0.260 20000 ; THR7
20 21 1 0.260 20000 ; THR9
26 27 1 0.260 20000 ; THR12
28 29 1 0.310 20000 ; ILE13
30 31 1 0.260 20000 ; THR14
36 37 1 0.265 20000 ; VAL17
46 47 1 0.260 20000 ; THR22
48 49 1 0.310 20000 ; ILE23

....
...
....

When I try to run mdrun for equilibrate the solvent or for the whole protein without equilibrate the solvent before,

mdrun -f example.mdp -c md1.pdb -g md1.log &


I obtain a segmentation fault as result.

For 20 ps

Back Off! I just backed up md1.log to ./#md1.log.4#
Reading file topol.tpr, VERSION 4.0.7 (single precision)

Back Off! I just backed up traj.trr to ./#traj.trr.7#

Back Off! I just backed up traj.xtc to ./#traj.xtc.7#

Back Off! I just backed up ener.edr to ./#ener.edr.7#
starting mdrun 'protein in water'
10000 steps, 20.0 ps.

Step 1 Warning: pressure scaling more than 1%, mu: 20.6639 20.6639 28.1722

[1]+ Segmentation fault mdrun -f example.mdp -c md1.pdb -g md1.log


For 200 ps

Back Off! I just backed up md1.log to ./#md1.log.5#
Reading file topol.tpr, VERSION 4.0.7 (single precision)

Back Off! I just backed up traj.trr to ./#traj.trr.8#

Back Off! I just backed up traj.xtc to ./#traj.xtc.8#

Back Off! I just backed up ener.edr to ./#ener.edr.8#
starting mdrun 'protein in water'
10000 steps, 200.0 ps.

[1]+ Segmentation fault mdrun -f example2.mdp -c md1.pdb -g md1.log
melchor@blauet:~/CSIC/calculos/Martini/Prueba$

My mdp file is like this:

title = Martini tutorial protein in water
cpp = /usr/bin/cpp

integrator = md
tinit = 0.0
dt = 0.02
nsteps = 10000
nstcomm = 1
comm-grps =

nstxout = 10000
nstvout = 10000
nstfout = 0
nstlog = 10000
nstenergy = 10000
nstxtcout = 1000
xtc_precision = 100
xtc-grps =
energygrps = protein W
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.2

coulombtype = PME ; SHIFT
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 2.5
vdw_type = shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tcoupl = Berendsen
tc-grps = protein W
tau_t = 0.1 0.1
ref_t = 320 320
Pcoupl = berendsen
Pcoupltype = semiisotropic
tau_p = 1.0 1.0
compressibility = 3e-4 3e-4
ref_p = 1.0 1.0

gen_vel = no
gen_temp = 320
gen_seed = 473529
constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30


I have revised forums at internet,web pages, Gromacs manual, etc and I don't know what can I do. If you can suggest me a form of solve my problem I will be very pleasure.

Grettings,

Melchor S.

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12 years 10 months ago #729 by Melchor
Replied by Melchor on topic Warning: atom names in .top and .pdb do not match
I had minimized the structure , doing:

grompp -v -f minimization.mdp -c 2.pdb -p 1UBQ.top -o minimization.tpr -maxwarn 200


mdrun -v -s minimization.tpr -o minimization.trr -c minimization.pdb -e minimization.edr

My problem is that I try to reproducethe steps that I normally use for carry out all-atom MD simulations, but for CG models, and I can't do it.

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12 years 10 months ago #730 by Melchor
Replied by Melchor on topic Warning: atom names in .top and .pdb do not match
Thank you for all.

I just finish the tutorial and the Md-CG simulations without having problems.

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12 years 10 months ago #733 by xavier
Replied by xavier on topic Warning: atom names in .top and .pdb do not match

Melchor wrote: Thank you for all.

I just finish the tutorial and the Md-CG simulations without having problems.


cool,
XAvier.

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