MMPBSA.py gives you the flexibility to adjust any input file that is created
in arbitrary ways (noting that we won't be able to predict errors based on
your input). The manual details how to use the -use-mdins flag in
conjunction with the -make-mdins flag in order to do what you're trying to
do.
For the perl version you'll have to manually edit the
mm_pbsa_createinput.pm(I think that's the one) package and add those
variables to the &pb namelist
of the PB input file.
A highly updated (and much-improved) version of MMPBSA.py is about to be
released that will make installing and using MMPBSA.py much easier (as well
as much more flexible).
Hope this helps,
Jason
On Tue, Mar 15, 2011 at 6:34 AM, Osman, Roman <roman.osman.mssm.edu> wrote:
> Hi Dwight,
> I'm using the peel version. I didn't know I can do it with the python
> version.
> Thanks.
> Rami
>
> Sent from my iPhone
>
> On Mar 14, 2011, at 11:28 PM, "Dwight McGee" <dwight.mcgee.gmail.com>
> wrote:
>
> > Are you using the python or perl version of MMPBSA?
> >
> > On Mon, Mar 14, 2011 at 11:20 PM, Roman Osman <roman.osman.mssm.edu>
> wrote:
> >
> >> Hi,
> >> I am trying to calculate MMPBSA with the IVCAP = 1; CUTCAP = 15.0
> >> I am getting the following message in pbsa_com.1.out:
> >>
> >> | Flags:
> >> cap water should only be run with eneopt=1 and frcopt=0
> >>
> >> How do I set these parameters in the input?
> >>
> >> Thanks for your help,
> >> Rami Osman
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > T. Dwight McGee Jr.
> > Quantum Theory Project
> > University of Florida
> > Graduate Student
> > dwight.mcgee.gmail.com
> >
> > "Problems cannot be solved at the same level of awareness that created
> > them."
> > Albert Einstein
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 15 2011 - 08:00:07 PDT
