[gmx-users] [ constraints ] in .rtp database not recognized by pdb2gmx

Justin Lemkul jalemkul at vt.edu
Fri Feb 13 22:40:33 CET 2015

On 2/13/15 11:34 AM, Barnett, James W wrote:
> I'm using fixed bond lengths from TRAPPE-UA with [ constraints ] type 1. I'm attempting to place constraints in an .rtp file for use with pdb2gmx, but it looks like GROMACS doesn't recognize the keyword in that case. It thinks it is a new residue name:
> Fatal error:
> in .rtp file in residue constraints at line:
>     C1    C
> This is my .rtp file<https://gist.githubusercontent.com/wesbarnett/93b27158fd49994eeac4/raw/845c56be6e4f0374c4ade7b901ec76f7184ba38b/npa.rtp>. The force field is set up properly, since when I replace "[ constraints ] " with "[ bonds ] " pdb2gmx works fine (after which I manually change [ bonds ] to [ constraints ] in the generated topol.top file and am able to run the simulation normally).
> Is the [ constraints ] directive supported for pdb2gmx? I've searched the manual but don't see if this is supported.

Not supported.  Only bonds, angles, dihedrals, impropers, exclusions, and cmap 
are valid.  It's easy to add support for more directives, though.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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