On Sun, Sep 20, 2015, Francesco Pietra wrote:
>
> My aim is to get the FF for a protein bearing the two ligands. As far as I
> know leap does not read parm7/rst. Also, as far as I know, running
> parm7/rst with NAMD (which I intend to do, having no recent amber version,
> nor money for that) requires a single parm7/rst.Thanks for suggesting a
> procedure.
Use LEaP to read in the mol2 or off files you create for each ligand
separately; load the corresponding frcmod files (if any); load a pdb file
with the protein + both ligands; output a parm7/rst7 combination that has
everything. Give that to NAMD, paying attention to the instructions here:
http://ambermd.org/namd/namd_amber.html
...good luck....dac
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Received on Sun Sep 20 2015 - 06:00:06 PDT
