[gmx-users] analysing charmm trajectories

Justin Lemkul jalemkul at vt.edu
Wed Jan 14 00:43:14 CET 2015

On 1/13/15 8:18 AM, Chiara Parravicini wrote:
> Dear all,
> I'd like to use the gromacs analysis tool to analyse a simulation performed
> with charmm.
> I installed the latest gromacs version (5.0.4), in which both .dcd
> trajectories and all the files read also by vmd should be readable. After
> that, the trajectory is correctly processed by gromacs, but I've troubles
> with the analysis tools that need .tpr files.
> As suggested in some previous posts, I've generated a fake file .top with
> vmd, useful to produce a new .tpr suitable for the analysis. I also
> installed the charmm36 forcefield in the gmx top directory (the same that I
> used in the simulation).
> When I use grompp to generate a .tpr, I get this error:
> Fatal error:
> Unknown cmap torsion between atoms 5 7 9 22 24
> Among the possible solutions I found the use of this patch, but this was
> concerning an older vs of gromacs: “0001-Fix-pdb2gmx-merge-cmap.patch”, so
> I skipped it during installation.
> I do not understand if this error it's a matter of forcefield or it depends
> on something else. Does anyone could help me to figure-out the origin of
> the error and how to fix the problem?
> Also pdb2gmx is not working because some atoms are not found in the
> forcefield (such as CAY, used by charmm for methylated methionine).
> Manipulating the forcefield would fix both the problems? In this case how
> should I proceed?
> I'd really appreciate any suggestion!

So the .top that VMD wrote is probably wrong in some way, but if you're just 
using it to do analysis and not actually run a simulation, I'd say you can 
probably remove the offending CMAP term from the .top and proceed.



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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