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

[Christian Blau]

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
>