[gmx-users] Using x2top and grompp

[Mark Abraham]

Hi,

First, choose a force field that can model your system accurately. Second,
use the right tool for generating a topology for that force field. Third,
as Justin said, nobody can help with that unless you share the actual
errors - copy and paste!

But you need to grapple with the first two questions before that matters,
and probably get some experience doing tutorials and study some easier
systems first.

Mark

On Sat, 1 Oct 2016 04:50 Devon Dillon <devondillon333 at gmail.com> wrote:

>
> >
> >> My goal is to get a topology.tpr and trajectory.xtc in those file
> formats. I’m starting off with .pdb, .xyz, and .gro files of an
> experimentally determined crystal structure. The crystal contains two kinds
> of molecules that interact via halogen bonding. i do not want to run these
> molecules in a solvent. when ever i submit a job to x2top i get a fatal
> error stating it could not find a forcefield for all of the atoms and
> terminates. when using pdb2gmx i get an input/output error then it states
> the (name of the file .pdb.gro). I have tried to selecting all of the
> different force fields what can i do to fix my problem?
> >> Thank you
>
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