On Thu, Feb 26, 2015 at 1:08 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Jason,
>
> apologies for getting back to you on this again.
>
> I’ve run the script. The terminal output is shown here:
>
> Shouldn’t there be a complex.prmtop produced as well? According to the
> help file, one should also get a prmtop of the stripped complex.
>
> $ ante-mmpbsa.py -p 4fqt_solv.prmtop -c complex.prmtop -r receptor.prmtop
> -l ligand.prmtop -n :126 --radii=mbondi2
>
>
Creating receptor topology file by stripping :126 from 4fqt_solv.prmtop
> Done creating receptor topology file!
>
> Creating ligand topology file by stripping !(:126) from 4fqt_solv.prmtop
> Done creating ligand topology file!
>
Ack, sorry, I got my default behaviors messed up. There is no default
--strip-mask value. If no strip mask is given, it assumes you don't want
anything stripped from the -p prmtop file.
You can just take the default strip_mask from MMPBSA.py (you can get it
from MMPBSA.py --input-file-help):
ante-MMPBSA.py -p 4fqt_solv.prmtop
-s :WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F -c complex.prmtop ...
Note that on a Mac, "ante-mmpbsa.py" will work because the filesystem is
case-insensitive. But the actual binary name is ante-MMPBSA.py, and on
Linux machines the case matters.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 26 2015 - 12:00:02 PST
