[gmx-users] pdb2gmx and virtual sites

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 4 20:07:38 CET 2009

Ondrej Marsalek wrote:
> Dear GROMACS users,
> I would like to substitute hydrogens in a protein with virtual sites
> to allow for the 4-5 fs timestep mentioned in the GROMACS 4 paper and
> several other places. So far, I have not found an example or a
> tutorial that would involve this, so I want to create a
> straightforward example. I have taken the 2KO3 structure from the PDB
> and went through this sequence of commands:
> pdb2gmx -v -f 2KO3.pdb -o initial-vacuum.gro -ff oplsaa -water tip4p
> -vsite hydrogens -ignh
> editconf -f initial-vacuum.gro -o initial-box.gro -c -d 1 -bt cubic
> genbox -cp initial-box.gro -cs tip4p.gro -p topol.top -o conf.gro
> grompp
> I also provided a pretty standard grompp.mdp, that contains
> "constraints = h-angles". I get the following error:
> -------------------------------------------------------
> Program grompp, VERSION 4.0.5
> Source code file: vsite_parm.c, line: 779
> Fatal error:
> Automatic parameter generation not supported for Virtual site 3 atom 4
> for this bonding configuration
> -------------------------------------------------------
> I am not sure what the problem is. I would appreciate and help on the
> use of this feature, pointers to resources, or a working example.
> Reading the manual and searching did not help as much as I would like.

Have you tried specifying either "all-bonds" or "h-bonds" for constraints?  I 
think "all-bonds" is the most commonly-used option.  Any specific reason for 
using "h-angles"?


> Thanks,
> Ondrej
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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