Hi,
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 Final.top crdname Final
crdout Final Final.mol2
Hope this helps,
-Dan
On Sat, Feb 2, 2019 at 12:10 PM Stefano Guglielmo
<stefano.guglielmo.unito.it> 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
>
> --
> Stefano GUGLIELMO PhD
> 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
