VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Wed Aug 05 2020 - 11:54:56 CDT

Hi Ethan,

Does it work if you delete the [cmap] section from the output .top file? Or
add in the charmm parameters for giggles when making the .top file? Grompp
is complaining about the crossterm/CMAP correction in the psf, which is a
perfectly normal thing for a protein model to have, but *maybe* it is
complaining that there aren't parameters for the interaction it is trying
to make. If neither of the first two options work for you, would you mind
sending your inputs so I can dig a bit deeper?

-Josh

On Wed, Aug 5, 2020 at 9:56 AM Ethan Croitoru <ecroitoru1_at_gmail.com> wrote:

> 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
>