> On Jun 16, 2015, at 10:41 PM, Chris <dlutlife223.163.com> wrote:
>
> Dear all:
>
> I have a solvated prmtop file : com_sol.prmtop, and I want calculate MM-PBSA energy, so I use ante-MMPBSA.py to prepare
> my prmtop files for ligand, receptor and complex.
>
> First I run:
>
> ante-MMPBSA.py -p com_sol.prmtop -s "!(:1-252)" -c com.prmtop
>
> it successfully generate complex prmtop file: com.prmtop
>
> Next, I should extract receptor and ligand from com.prmtop
>
> I run:
> ante-MMPBSA.py -p com.prmtop -m ":1-250" -r rec.prmtop
> ante-MMPBSA.py -p com.prmtop -n ":251-252" -l rec.prmtop
You should do this all with one step:
ante-MMPBSA.py -p com_sol.prmtop -s "!(:1-252)" -c com.prmtop -m ":1-250" -r rec.prmtop -l lig.prmtop
>
>
> error comes:
> ----------
> Error: You specified ligand or receptor mask, but not a ligand and receptor topology file!
> ---------
> I don't know how to do it if I understanding the manual correctly.
ante-MMPBSA.py generates *all* of the topology files you need in one step.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 16 2015 - 22:30:02 PDT
