normal backward.py problem determining mapping coordinates

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1 year 3 weeks ago #7643 by sdixit
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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1 year 2 weeks ago - 1 year 2 weeks ago #7646 by riccardo
What are the atom names in the "cg_iappdimer_antiparallel.pdb" file for the residue LYS?
Last edit: 1 year 2 weeks ago by riccardo.

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1 year 2 weeks ago #7648 by sdixit
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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1 year 2 weeks ago #7649 by riccardo
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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1 year 2 weeks ago #7650 by sdixit
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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1 year 1 week ago #7657 by riccardo
mm, not sure then. Is there any atom labeled CE1 in your topology file?

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1 year 1 week ago #7658 by sdixit
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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1 year 1 week ago #7659 by riccardo
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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1 year 1 week ago #7660 by sdixit
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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1 year 1 week ago #7661 by riccardo
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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8 months 2 weeks ago #7797 by z.sichaib
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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8 months 2 weeks ago #7801 by tsjerk
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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7 months 3 weeks ago #7815 by z.sichaib
Thank you very much! I will investigate the problem.

Best,

Zeineb

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7 months 3 weeks ago #7822 by z.sichaib
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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7 months 1 week ago #7831 by riccardo
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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1 month 4 days ago #8097 by kristina.woods
Replied by kristina.woods on topic backward.py problem determining mapping coordinates
What was the solution to this issue? I don't see the solution posted in further posts. I have the same problem.

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1 month 3 days ago #8104 by riccardo
Not sure how it got solved - z.sichaib hopefully will tell us.

Otherwise: which problem are you at in particular? The memory error?
Have you successfully backmapped the system in some conformation like z.sichaib?

Also, make sure you use the latest backward version (available on GitHub: github.com/Tsjerk/Backward ).

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1 month 3 days ago #8106 by z.sichaib
Dear Kristina,

What is the exact error that you are obtaining?

1- If your backmapping is crashing with this error:
'File '2-EM.gro' does not exist or is not accessible
Reason: No such file or directory' --> In this case, the backmapping generates a structure but the minimization fails

I fixed it by just running the same command line again (you can even try several times).

2- If you are getting the error of the memory. In my case, I was running the backmapping on a supercomputer and I fixed it by using another "variant" of Gromacs.

Zeineb

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1 month 3 days ago #8109 by kristina.woods
Replied by kristina.woods on topic backward.py problem determining mapping coordinates
Hi Zeineb,

I apologize for such a vague description of my problem. My issue is similar to the original post on this topic thread.

When using backward to convert my CG system back to an atomistic system using the following command:

backward/initram.sh -f protein.gro -p ../../../MetaII_charmm36.top -o out.gro -from martini -to charmm36

I get the following error:
Checking dependencies:
backward.py ... /Users/kristina/Documents/md_simulations/protein_dynamics/rhodopsin/Meta_II/MetaII_long/rhodopsin_6/backward/backward.py
grompp ... /usr/local/gromacs/bin/grompp
mdrun ... /usr/local/gromacs/bin/mdrun
Residues defined for transformation from martini to charmm36:

Problem determining mapping coordinates for atom CZ of residue SER.
atomlist:
want: CZ
have:
Bailing out...



The error is confusing for a few different reasons:
- There is no CZ in SER. There is a CZ in other residues - and in particular the error refers to residue PHE (which has a CZ) and not SER. So somehow the program recognizes PHE as SER.

- I have checked the numbering in my atomistic topology and it does not differ from the numbering/residues in my CG coordinates

- The backward mapping files are in the correct place

- Perhaps it's also important to note that the original CG system was created with martinize.py using the elendyn forcefield

- I am not sure what information I should give that would be helpful.

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3 weeks 6 days ago #8123 by riccardo
.. it seems that you checked already many things.!
I guess the only way (I can think of) that backward can recognize PHE as SER is if there's a mismatch between the order of the residues in the CHARMM topology and in the Martini coordinates - but you checked that and that's not the case.. Do you actually have a SER close to a PHE in the protein? Maybe looking at the AA topology or CG coordinates around that point gives us some hints?

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