On Tue, 2014-04-22 at 14:43 +0400, James Starlight wrote:
> This issue has been solved by the below corrections
>
> chamber -top ./toppar/top_all36_prot.rtf
> -param ./toppar/par_all36_prot.prm -psf step1_pdbreader.psf -crd
> step1_pdbreader.pdb
> -str ./toppar/par_all36_cgenff.prm ./toppar/p0g.prm -nocmap
>
>
> Now converting 2 psf files I obtain 2 prmtop files corresponded to the
> 1) solvated complex included membrane and 2) dry complex of
> protein-ligand atoms only.
>
> Taking as the input dry complex I'd like to create 2 additional
> prmtops for the ligand and protein separately using
> ante-MMPBSA.py -p complex_dry.prmtop -r receptor -l ligand -n
>
>
> How I should specify ligand mask properly ? E.g I ligand is the 1
> residues with the name p0g. Trying ante-MMPBSA.py -p
> complex_dry.prmtop -r receptor -l ligand -n p0g
This should be "-n :p0g" -- notice the colon. This is the standard
Amber mask syntax (used in most Amber programs and described in the
Amber manual in one of the Appendices).
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 22 2014 - 04:30:02 PDT
