VMD-L Mailing List

From: Ethan Croitoru (ecroitoru1_at_gmail.com)
Date: Wed Aug 05 2020 - 10:23:49 CDT

Hello,

I have a NAMD simulation (i.e. dcd and psf files), and would like to use
some of GROMACS trajectory analysis commands. In order to do so I need a
sudo .tpr file, one that's good enough for analysis, but won't work for
simulation. I have been following the steps outlined here:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2003-2012/14046.html
So I have a .top file from using the vmd plugin topo (
http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/), but when I try to
execute this gmx grompp command:

gmx grompp -f sample.mdp -c structure.pdb -p structure.top -o simulation.tpr

I get:

Fatal error:
Unknown cmap torsion between atoms 13 15 17 23 25

I have seen this can be an issue with the .top file used, so to create that
I ran:

topo writegmxtop structure.top

with the psf and pdb files loaded into vmd. From my understanding, I don't
need to add parameter files since I won't be running simulations with these
files.
Any help with this error would be appreciated.

Best,
Ethan