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

[Billy Williams-Noonan]

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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Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

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