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

Barnett, James W jbarnet4 at tulane.edu
Fri Feb 13 17:34:57 CET 2015

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.


James "Wes" Barnett

Ph.D. Candidate

Chemical and Biomolecular Engineering

Tulane University

Boggs Center for Energy and Biotechnology, Room 341-B

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