normal backward.py problem determining mapping coordinates

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6 months 1 week ago #7643 by sdixit
sdixit created the topic: backward.py problem determining mapping coordinates
Hi,

I'm trying to convert coarse grain model to all atom model using initram.sh and backward.py. First, initram.sh always fail.
Here's the output from the terminal:

(py27) [sugyan@bruotolo-serv test_cg]$ ./initram.sh -f cg_iappdimer_antiparallel.pdb -p topol.top -o backmapped.gro -po backmapped.top -to charmm36

./initram.sh -f cg_iappdimer_antiparallel.pdb -p topol.top -o backmapped.gro -po backmapped.top -to charmm36

GROMACS VERSION:
MPI: false
./initram.sh: line 305: /home/sugyan/Documents/charmm/workfolder/membraneproteinsimulation/test_cg backward.py -f cg_iappdimer_antiparallel.pdb -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to charmm36 -solname SOL: No such file or directory

gmx grompp -f 1-EM.mdp -c 0-backward.gro -n backmapped.ndx -p backmapped.top -o 1-EM -maxwarn 2

Program: gmx grompp, version 2018-rc1
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 235)
Function: void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
In command-line option -c
File '0-backward.gro' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
In command-line option -n
File 'backmapped.ndx' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)


From that error it looks like the backward.py was not running properly and didn't generate any files necessary to run gromacs.

So I just executed backward.py to see what happens
This is the output:

(py27) [sugyan@bruotolo-serv test_cg]$ python backward.py -f cg_iappdimer_antiparallel.pdb -o backmapped.gro -p topol.top -po backmapped.top -to charmm36 -mapdir Mapping
Residues defined for transformation from martini to charmm36:

chiral
chiral
chiral
......
chiral
Problem determining mapping coordinates for atom CE1 of residue LYS.
atomlist:
want: CE1
have:
Bailing out...


This made me think that there's probably issues in different nomenclature of certain beads in the coarse grained (cg) .pdb file and .top/.itp.

The way I'm creating my cg .pdb file is using martinize.py. It does give me the following WARNING:

[sugyan@bruotolo-serv test_cg]$ python martinize.py -f iappdimer_antiparallel.gro -o cg_topol.top -x cg_iappdimer_antiparallel.pdb -dssp /usr/local/bin/dssp -ff martini22p
INFO MARTINIZE, script version 2.6_3
INFO If you use this script please cite:
INFO de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO The martini22p forcefield will be used.
INFO Local elastic bonds will be used for extended regions.
INFO Read input structure from file.
INFO Input structure is a GRO file. Chains will be labeled consecutively.
INFO Found 2 chains:
INFO 1: A (), 548 atoms in 37 residues.
INFO 2: B (), 548 atoms in 37 residues.
INFO Total size of the system: 74 residues.
INFO Writing coarse grained structure.
INFO (Average) Secondary structure has been determined (see head of .itp-file).
INFO Created coarsegrained topology
INFO Created coarsegrained topology
INFO Written 2 ITP files
INFO Output contains 2 molecules:
INFO 1-> Protein_A (chain A)
INFO 2-> Protein_B (chain B)
INFO Written topology files
WARNING Bead names of charges in sidechains differ between .top/.itp and .pdb.
WARNING Using names in topology, as Gromacs does, gives the correct result.


I'm not sure how to resolve this or whether I should be doing things differently. Any help would be greatly appreciated. Thanks!

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6 months 1 week ago - 6 months 1 week ago #7646 by riccardo
riccardo replied the topic: backward.py problem determining mapping coordinates
What are the atom names in the "cg_iappdimer_antiparallel.pdb" file for the residue LYS?
Last Edit: 6 months 1 week ago by riccardo.

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6 months 1 week ago #7648 by sdixit
sdixit replied the topic: backward.py problem determining mapping coordinates
ATOM 1 BB LYS 1 -6.835 -21.627 -1.737 1.00 0.00 B
ATOM 2 SC1 LYS 1 -4.670 -21.113 0.117 1.00 0.00 S
ATOM 3 SC2 LYS 1 -4.197 -20.075 2.530 1.00 0.00 S
ATOM 4 SCD LYS 1 -4.290 -20.019 2.547 1.00 0.00 S

Those are the atom names for Lys residue.

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6 months 6 days ago #7649 by riccardo
riccardo replied the topic: backward.py problem determining mapping coordinates
I'm trying to figure out what gives you the error:

Problem determining mapping coordinates for atom CE1 of residue LYS.
atomlist:
want: CE1
have:
Bailing out...


If you get the backward archive from:

cgmartini.nl/images/tools/backward/backward-v5.zip

then the lys.charmm36.map does not contain any "CE1" atom. Does your (charmm) atomistic topology - which you specify via "topol.top" - contain an atom labelled "CE1" in lys?

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6 months 5 days ago #7650 by sdixit
sdixit replied the topic: backward.py problem determining mapping coordinates
It does not have atom labelled CE1 in the topoly file. Here's the info on Lys residue from the topology file

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 LYS rtp LYS q +2.0
1 NH3 1 LYS N 1 -0.3 14.007 ; qtot -0.3
2 HC 1 LYS H1 2 0.33 1.008 ; qtot 0.03
3 HC 1 LYS H2 3 0.33 1.008 ; qtot 0.36
4 HC 1 LYS H3 4 0.33 1.008 ; qtot 0.69
5 CT1 1 LYS CA 5 0.21 12.011 ; qtot 0.9
6 HB 1 LYS HA 6 0.1 1.008 ; qtot 1
7 CT2 1 LYS CB 7 -0.18 12.011 ; qtot 0.82
8 HA 1 LYS HB1 8 0.09 1.008 ; qtot 0.91
9 HA 1 LYS HB2 9 0.09 1.008 ; qtot 1
10 CT2 1 LYS CG 10 -0.18 12.011 ; qtot 0.82
11 HA 1 LYS HG1 11 0.09 1.008 ; qtot 0.91
12 HA 1 LYS HG2 12 0.09 1.008 ; qtot 1
13 CT2 1 LYS CD 13 -0.18 12.011 ; qtot 0.82
14 HA 1 LYS HD1 14 0.09 1.008 ; qtot 0.91
15 HA 1 LYS HD2 15 0.09 1.008 ; qtot 1
16 CT2 1 LYS CE 16 0.21 12.011 ; qtot 1.21
17 HA 1 LYS HE1 17 0.05 1.008 ; qtot 1.26
18 HA 1 LYS HE2 18 0.05 1.008 ; qtot 1.31
19 NH3 1 LYS NZ 19 -0.3 14.007 ; qtot 1.01
20 HC 1 LYS HZ1 20 0.33 1.008 ; qtot 1.34
21 HC 1 LYS HZ2 21 0.33 1.008 ; qtot 1.67
22 HC 1 LYS HZ3 22 0.33 1.008 ; qtot 2
23 C 1 LYS C 23 0.51 12.011 ; qtot 2.51
24 O 1 LYS O 24 -0.51 15.999 ; qtot 2

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6 months 10 hours ago #7657 by riccardo
riccardo replied the topic: backward.py problem determining mapping coordinates
mm, not sure then. Is there any atom labeled CE1 in your topology file?

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6 months 10 hours ago #7658 by sdixit
sdixit replied the topic: backward.py problem determining mapping coordinates
Yes, PHE and TYR has CE1 on the topology file. See below for details from the topology file:
; residue 15 PHE rtp PHE q 0.0
205 NH1 15 PHE N 205 -0.47 14.007 ; qtot 2.53
206 H 15 PHE HN 206 0.31 1.008 ; qtot 2.84
207 CT1 15 PHE CA 207 0.07 12.011 ; qtot 2.91
208 HB 15 PHE HA 208 0.09 1.008 ; qtot 3
209 CT2 15 PHE CB 209 -0.18 12.011 ; qtot 2.82
210 HA 15 PHE HB1 210 0.09 1.008 ; qtot 2.91
211 HA 15 PHE HB2 211 0.09 1.008 ; qtot 3
212 CA 15 PHE CG 212 0 12.011 ; qtot 3
213 CA 15 PHE CD1 213 -0.115 12.011 ; qtot 2.885
214 HP 15 PHE HD1 214 0.115 1.008 ; qtot 3
215 CA 15 PHE CE1 215 -0.115 12.011 ; qtot 2.885
216 HP 15 PHE HE1 216 0.115 1.008 ; qtot 3
217 CA 15 PHE CZ 217 -0.115 12.011 ; qtot 2.885
218 HP 15 PHE HZ 218 0.115 1.008 ; qtot 3
219 CA 15 PHE CD2 219 -0.115 12.011 ; qtot 2.885
220 HP 15 PHE HD2 220 0.115 1.008 ; qtot 3
221 CA 15 PHE CE2 221 -0.115 12.011 ; qtot 2.885
222 HP 15 PHE HE2 222 0.115 1.008 ; qtot 3
223 C 15 PHE C 223 0.51 12.011 ; qtot 3.51
224 O 15 PHE O 224 -0.51 15.999 ; qtot 3

; residue 37 TYR rtp TYR q -1.0
527 NH1 37 TYR N 527 -0.47 14.007 ; qtot 3.53
528 H 37 TYR HN 528 0.31 1.008 ; qtot 3.84
529 CT1 37 TYR CA 529 0.07 12.011 ; qtot 3.91
530 HB 37 TYR HA 530 0.09 1.008 ; qtot 4
531 CT2 37 TYR CB 531 -0.18 12.011 ; qtot 3.82
532 HA 37 TYR HB1 532 0.09 1.008 ; qtot 3.91
533 HA 37 TYR HB2 533 0.09 1.008 ; qtot 4
534 CA 37 TYR CG 534 0 12.011 ; qtot 4
535 CA 37 TYR CD1 535 -0.115 12.011 ; qtot 3.885
536 HP 37 TYR HD1 536 0.115 1.008 ; qtot 4
537 CA 37 TYR CE1 537 -0.115 12.011 ; qtot 3.885
538 HP 37 TYR HE1 538 0.115 1.008 ; qtot 4
539 CA 37 TYR CZ 539 0.11 12.011 ; qtot 4.11
540 OH1 37 TYR OH 540 -0.54 15.999 ; qtot 3.57
541 H 37 TYR HH 541 0.43 1.008 ; qtot 4
542 CA 37 TYR CD2 542 -0.115 12.011 ; qtot 3.885
543 HP 37 TYR HD2 543 0.115 1.008 ; qtot 4
544 CA 37 TYR CE2 544 -0.115 12.011 ; qtot 3.885
545 HP 37 TYR HE2 545 0.115 1.008 ; qtot 4
546 CC 37 TYR C 546 0.34 12.011 ; qtot 4.34
547 OC 37 TYR OT1 547 -0.67 15.9994 ; qtot 3.67
548 OC 37 TYR OT2 548 -0.67 15.9994 ; qtot 3

If I now go to the mapping files (.map) for these residues, they do contain CE1 as well.

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6 months 10 hours ago #7659 by riccardo
riccardo replied the topic: backward.py problem determining mapping coordinates
I wonder why backward sees an atom CE1 as being part of LYS.

Is there any order mismatch between the residues in the atomistic topology and in the "cg_iappdimer_antiparallel.pdb" (i.e., LYS should be residue 1 in both the itp and pdb, PHE should be residue 15 in both, etc.)?

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6 months 10 hours ago #7660 by sdixit
sdixit replied the topic: backward.py problem determining mapping coordinates
Yes I checked that, there is no mismatch between the residue number in topology file and cg_iappdimer_antiparallel.pdb file.

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6 months 10 hours ago #7661 by riccardo
riccardo replied the topic: backward.py problem determining mapping coordinates
Can you send the files (all the necessary for the backmapping) to This email address is being protected from spambots. You need JavaScript enabled to view it.? I will give it a try.

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2 months 1 week ago #7797 by z.sichaib
z.sichaib replied the topic: backward.py problem determining mapping coordinates
Hi,

I'm getting the same error but at a different stage:
******************
Error in user input:
Invalid command-line options
In command-line option -c
File '2-EM.gro' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory
(call to fopen() returned error code 2)
**************
It seems that at the beginning backward is working for me but then at 2-EM it generates all the files (tpr, trr, edr, log) except the gro one.

Did you fix your problem? if Yes, can you tell we where was the issue for you, please? maybe it will help me to fix mine.

Best

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2 months 6 days ago #7801 by tsjerk
tsjerk replied the topic: backward.py problem determining mapping coordinates
Hi,

This is a very different problem. Here backward did run correctly and generated a structure, but the energy minimization failed. Please check the log of that step. Problems in the energy minimization can often be resolved by trying again, unless there is a problem with a (nonstandard) mapping.

Best,

Tsjerk

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1 month 1 week ago #7815 by z.sichaib
z.sichaib replied the topic: backward.py problem determining mapping coordinates
Thank you very much! I will investigate the problem.

Best,

Zeineb

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1 month 1 week ago #7822 by z.sichaib
z.sichaib replied the topic: backward.py problem determining mapping coordinates
Dear Tsjerk,

I still have the same problem: backmapping crashed with the following final error:
Program: gmx grompp, version 2016.4
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 235)
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -c
File '3-mdpr-0.0002.gro' does not exist or is not accessible.
The file could not be opened.
Reason: No such file or directory

When I check the log file, I noticed that during the minimization there were many Links warnings and at some point, there was also this error message (before the previous one):

Fatal error:
Not enough memory. Failed to realloc 509248 bytes for nlist->jjnr,
nlist->jjnr=54eb59a0
(called from file
/usr/local/software/jureca/Stages/2017b/build/GROMACS/2016.4/gmvolfc-2017b-GDR-hybrid/gromacs-2016.4/src/gromacs/mdlib/ns.cpp,
line 476)

I run the back mapping on the same file several times but still getting the same error.

What do you mean by "a problem with a (nonstandard) mapping"?.

NB: I successfully backmapped the same system (but different conformation of the protein) without any problems.

Thank you in advance for your help.

Zeineb

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4 weeks 2 days ago #7831 by riccardo
riccardo replied the topic: backward.py problem determining mapping coordinates
Hi Zeineb,

What Tsjerk meant with "nonstandard mapping" is a mapping file which is *not* included with the backward tarball you can download from cgmartini.nl but that you, for example, created yourself.

Since you could backmap the same system successfully, perhaps there's no problems with the mapping files even if you are using nonstandard ones.
I am not sure about the memory error - never seen it - but otherwise I would still believe that your problem is due to the energy minimizations not converging properly so that the first equilibration step gives you a lot of LINCS warnings and then crashes.

Are the snapshot which is giving you problems and the snapshot that you could backmap successfully coming from the same trajectory? In any case, I would take a look (visually) at these two snapshots to check what is different. You could also have a look at the projected.gro and 0-backward.gro (or, 0-projected.gro and backward.gro, can't remember..) files which are produced by backward at the beginning of the backampping procedure in both cases and see whether anything looks different.

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