[gmx-users] analysing charmm trajectories

Chiara Parravicini parravicini.chiara at gmail.com
Tue Jan 13 14:18:53 CET 2015

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!

Thank you very much in advance!


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