Hello,
A couple modifications. This version of MMPBSA.py doesn't accept commas
inside input variables (the upcoming version fixes this issue).
Change to
receptor_mask=":1-28:57-84", ligand_mask=":29-56:85-112"
That should work.
Hope this helps,
Jason
On Fri, Mar 18, 2011 at 10:30 AM, Chris Chris <alpharecept.yahoo.com> wrote:
> Bill-
>
> Would this be correct then? :
>
>
> &general
> startframe=6000, endframe=8000, interval=1,
> verbose=2, keep_files=0, receptor_mask=':1-28,:57-84',
> ligand_mask=':29-56,:85-112'
> /
> &gb
> igb=2,
> /
> &pb
> fillratio=4.0,
> /
>
>
>
>
> ________________________________
> From: Bill Miller III <brmilleriii.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Fri, March 18, 2011 12:50:17 PM
> Subject: Re: [AMBER] trouble with mmpbsa.py
>
> Since the ligand residues are not sequential, MMPBSA.py will not be able to
> guess the proper residue numbers, so you will need to specify these by hand
> using the receptor_mask and ligand_mask variables in the MMPBSA.py input
> file.
>
> -Bill
>
> On Fri, Mar 18, 2011 at 12:44 PM, Chris Chris <alpharecept.yahoo.com>
> wrote:
>
> > I am trying to perform mmpbsa analysis using the python version of the
> > program
> > on the complex in the attachment but have been unable to do so.
> >
> > As can be seen in the complex scematic, the ligand and receptor are not
> > sequentially numbered. I thought this might be a problem so when I made
> the
> > topology files, I kept the numbering as it was in the original pdb which
> > was
> > used to make the topology files in xleap.
> >
> >
> > This was to no avail. Can anyone tell me what is going on here? Do I have
> > to
> > specify the residues in my .in file (see attached)?
> >
> > Thanks for any advice, I have also attached the .err and .out files as
> well
> >
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Mar 18 2011 - 11:00:04 PDT
