On Thu, 2015-02-26 at 14:16 -0300, George Tzotzos wrote:
> Jason,
>
> Many thanks for the prompt and very helpful reply.
>
> I’m interested in option 4: lB -- sA.sB and lA -- sA.lB.sB
>
> I had a quick look at ante-MMPBSA.py help. As I’ve never used the
> script before I’d be grateful for one additional clarification.
>
> Given the above option and that ligand lA is residue 126 of my current
> topology:
>
> 1. Is the following script correct?
>
> -p lA.sA.lB.sB_solv.prmtop -c lA.sA.lB.sB.prmtop -r sA.lB.sB.prmtop
> -l lA.prmtop -s :126 -n :126 --radii=mbondi2
No. -s/--strip-mask is the mask of atoms that you want to delete to go
from lA.sA.lB.sB_solv.prmtop --> lA.sA.lB.sB.prmtop. It serves the same
function as strip_mask in MMPBSA.py's input file.
So assuming you don't need to set strip_mask in MMPBSA.py, just take out
"-s :126".
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 26 2015 - 09:30:03 PST
