Re: [AMBER] merging molecules

From: Daniel Roe <>
Date: Mon, 4 Feb 2019 13:23:18 -0500


One thing you could try is loading the systems as COORDS data sets in
cpptraj, use 'combinecrd' to combine them, then write out a combined
mol2/pdb file that you can re-parameterize back in leap. Cpptraj does
do some combination of parameters but it hasn't been very thoroughly
tested which is why I wouldn't (yet) output a combined topology
directly. Something like:

parm protein.parm7
loadcrd protein.rst7 parm protein.parm7 name Protein
parm ligand.parm7
loadcrd ligand.rst7 parm ligand.parm7 name Ligand
combinecrd Protein Ligand parmname crdname Final
crdout Final Final.mol2

Hope this helps,


On Sat, Feb 2, 2019 at 12:10 PM Stefano Guglielmo
<> wrote:
> Dear Amber users,
> is there a way to merge two systems (eg a protein and a ligand) starting
> from two distinct prmtop files? I have googled a bit, trying to focus on
> ParmEd utility and it seemed that the combineMolecules command could fit,
> but I couldn't find the command in the version I have installed (3.0.3).
> Does anyone have any suggestions?
> Thanks
> Stefano
> --
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707178
> _______________________________________________
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Received on Mon Feb 04 2019 - 10:30:02 PST
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