[gmx-users] Fwd: Using amber-ff14SB forcefield port to GROMACS - blowing up error

[Mark Abraham]

Hi,

On Mon, Jun 12, 2017 at 7:14 PM p.kartheek <kartheekpitta at gmail.com> wrote:

> Dear experts,
> Currently I am trying to model Protein-DNA complex systems, with updated
> Amber forcefield parameters. Parmbsc1 for DNA and *ff14SB* for protein,
> considering the unavailability of theses updated forcefield ports within
> gromacs, I have managed to generate the topologies through tleap module of
> ambertools. Latter these topologies were translated to gromacs format using
> "ParmED". However, I am not able to proceed beyond minimization step due to
> hydrogen atoms related blowing up error.


Make sure you get your topologies working on single-molecule systems before
you try to get the whole complex working.

I want to do equilibration by
> applying restraints on only heavy atoms of the systems excluding hydrogens.
> But don't know how to generate posre files for only heavy atoms as the
> make_ndx doesn't showing any option to exclude hydrogens in water and DNA.
>

Don't restrain the water molecules - nothing much would relax if you did
that.


> I can use grep to get all the indices of hydrogens from the gro file but is
> there anyway to supply file where the information of heavy atoms is saved
> instead of entering values manually. Any kind of the help will be highly
> appreciated.
>

gmx select is a good way to generate an arbitrary selection in an index
file. Use that with gmx genrestr to make your position-restraint file.

Mark


> Thanks in advance.
>
> ----------------------------------------------
> P. Kartheek,
> PhD Candidate, Computational Biophysical Chemistry,
> Center for Computational Natural Sciences and Bioinformatics,
> International Institute of Information Technology,
> Marimuthu Krishan Group,
> 9701577399,
> kartheek.p at research.iiit.ac.in,
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