[gmx-users] Script to merge protein and ligand topology for BAR calculation?

[Billy Williams-Noonan]

Hi Christian,

Thank you for the link!  We have written a script locally, was wondering if
one existed elsewhere though!

Thanks again for your help,
Billy

On Wed, 13 Nov 2019 at 05:52, Christian Blau <blau at kth.se> wrote:

> Hi Billy,
>
>
> I cannot offer a script for the merging of the topologies, but depending
> on the transformation you want to carry out, I can suggest using pmx
>
> http://pmx.mpibpc.mpg.de/webserver.html
>
>
> for preparing dual topologies for alchemical free energy calculations
> that are GROMACS-compatible.
>
>
> Best,
>
> Christian
>
> On 2019-11-11 07:22, Billy Williams-Noonan wrote:
> > Hi Experts,
> >
> > I have a protein .itp file
> >
> > I -also- have the dual ligand .itp file to perform a relative alchemical
> > transformation
> >
> > Both are compatible with GROMACS, and use AMBER/GAFF parameters.
> >
> > I need a script that can easily merge the two together. Have been doing
> on
> > Excel. I was wondering if anyone would be kind enough to please share?
> >
> > FESetup is good, but the input requires correct atom naming for Amber
> (not
> > GROMACS) and this is a pain to get right.
> >
> > Cheers,
> > Billy
> >
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