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Bug #706

Virtual site generation broken for OPLS-AA

Added by Justin Lemkul over 8 years ago. Updated over 8 years ago.

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

Description

In version 4.5.3, virtual site generation fails with a fatal error for OPLS-AA. Take any .pdb file with histidine in it and run, i.e.:

pdb2gmx -f 1AKI.pdb -vsite hydrogens

...

-------------------------------------------------------
Program pdb2gmx, VERSION 4.5.3
Source code file: gen_vsite.c, line: 187

Fatal error:
Invalid directive HISD in vsite database /usr/local/gromacs/share/gromacs/top/oplsaa.ff/aminoacids.vsd
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Virtual site generation works for other force fields, like AMBER03 and CHARMM, since the HIS nomenclature works based on the hard-coded names in gen_vsite.c:

if(!gmx_strcasecmp(dirstr,"HID"))
sprintf(dirstr,"HISA");
else if(!gmx_strcasecmp(dirstr,"HIE"))
sprintf(dirstr,"HISB");
else if(!gmx_strcasecmp(dirstr,"HIP"))
sprintf(dirstr,"HISH");
curdir=ddb_name2dir(dirstr);
if (curdir < 0) {
gmx_fatal(FARGS,"Invalid directive %s in vsite database %s",
dirstr,ddbname);
}

I don't know whether the more elegant solution is to change the code, or make changes to the .r2b/.vsd/.rtp file(s).

History

#1 Updated by Justin Lemkul over 8 years ago

  • Assignee deleted (Berk Hess)

#2 Updated by Mark Abraham over 8 years ago

Does the aminoacids.r2b file fix this?

i.e. adding

HISA HISD
HISB HISE

Otherwise, the existing hackery seems to solve the AMBER case, so extending that hackery for OPLS/AA + ENCAD seems correct.

#3 Updated by Justin Lemkul over 8 years ago

Mark Abraham wrote:

Does the aminoacids.r2b file fix this?

i.e. adding

HISA HISD
HISB HISE

Nope, I still get the same fatal error.

Otherwise, the existing hackery seems to solve the AMBER case, so extending that hackery for OPLS/AA + ENCAD seems correct.

Perhaps so.

#4 Updated by Berk Hess over 8 years ago

  • Status changed from New to Feedback wanted
  • Assignee set to Berk Hess

We overlooked these dirty hardcoded names when implementing proper databases.
For 4.5.4 I added two histidine names, please try if it works now in release-4-5-patches
and report back.

Thanks,

Berk

#5 Updated by Justin Lemkul over 8 years ago

  • Status changed from Feedback wanted to Closed

Berk Hess wrote:

We overlooked these dirty hardcoded names when implementing proper databases.
For 4.5.4 I added two histidine names, please try if it works now in release-4-5-patches
and report back.

Yes, your fixes work. Thanks!

I'll go ahead and mark this one as closed.

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