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Bug #885

Multiple chains with charmm27 force field: Unknown cmap torsion between atoms

Added by neeraj agrawal about 5 years ago. Updated about 5 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
4.5.5
Affected version:
Difficulty:
uncategorized
Close

Description

$pdb2gmx -merge all -chainsep ter -ff amber99sb -water none -f 1aq5.pdb -o 1aq5.gro -p 1aq5.top
$grompp -f min_mdp -c 1aq5.gro> -p 1aq5.top -o min.tpr

and it works perfectly. However, when I replace amber99sb by charmm27, I get an error:

$pdb2gmx -merge all -chainsep ter -ff charmm27 -water none -f 1aq5.pdb -o 1aq5.gro -p 1aq5.top
$grompp -f min_mdp -c 1aq5.gro> -p 1aq5.top -o min.tpr

Error:

-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 1346

Fatal error:
Unknown cmap torsion between atoms 743 745 747 762 765

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

1aq5.pdb - http://gromacs.5086.n6.nabble.com/Interchain-Disulfide-Bond-td4488616.html (86.8 KB) neeraj agrawal, 02/21/2012 03:52 AM

min_run.mdp (360 Bytes) neeraj agrawal, 02/21/2012 03:52 AM

0001-Fix-pdb2gmx-merge-cmap.patch View - Patch file for bug fix (2.7 KB) Mark Abraham, 02/21/2012 07:24 AM


Related issues

Related to GROMACS - Bug #886: pdb2gmx -cmap needs some mention in manual section 5.6 Closed 02/21/2012

Associated revisions

Revision 4e4d743f (diff)
Added by Mark Abraham about 5 years ago

Fix pdb2gmx -cmap in corner cases

CMAP torsions are only generated when the atoms are from the same chain
(pdb2gmx -merge allows multiple chains to be present in the
moleculetype), and their residues are in residuetypes.dat as
"Protein".

Fixes #800, #885

Change-Id: Idc4f9a867beedc0be6a4c153606c0731eec86f5f

History

#1 Updated by Mark Abraham about 5 years ago

  • Category set to preprocessing (pdb2gmx,grompp)
  • Status changed from New to Feedback wanted
  • Assignee set to Mark Abraham
  • Target version set to 4.5.6

I think I fixed this. Please try the attached patch. From your GROMACS 4.5.5 source directory, use

patch -p1 -i 0001-Fix-pdb2gmx-merge-cmap.patch

and then make and make install in the usual way.

#2 Updated by Mark Abraham about 5 years ago

Added file

#3 Updated by neeraj agrawal about 5 years ago

Thanks Mark. It works for the single precision. Solves my issue !!

FYI, when I try to use pdb2gmx_d, I get the error: Making cmap torsions...Segmentation fault

#4 Updated by Mark Abraham about 5 years ago

neeraj agrawal wrote:

FYI, when I try to use pdb2gmx_d, I get the error: Making cmap torsions...Segmentation fault

Double precision should be irrelevant, and works for me. Did you rebuild the double precision version properly?

#5 Updated by Roland Schulz about 5 years ago

  • Status changed from Feedback wanted to Closed

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