Just to clarify, MMPBSA.py will only do a GB calculation if 1) the &gb
namelist is specified in the input file or 2) no other calculations (PB,
entropy, etc) are specified. So the mdcrd flag should not have any bearing
on whether a GB calculation is performed or not.
Regardless, glad to hear it works for you now.
-Bill
2011/5/12 Jesper Sørensen <lists.jsx.dk>
> Hi Bill,
>
> The mdcrd=0 flag tells it to not do GB (implicitly) as far as I can tell.
> But it works now - so thanks a lot.
>
> Best,
> Jesper
>
> -----Original Message-----
> From: Bill Miller III [mailto:brmilleriii.gmail.com]
> Sent: 12. maj 2011 13:27
> To: AMBER Mailing List
> Subject: Re: [AMBER] MMPBSA.py - entropy only?
>
> Using this very simple input file works for me.
>
> MMPBSA input file for using quasi-harmonic approximation for entropy
> &general
> keep_files=0, strip_mdcrd=0, entropy=1, /
>
> This should only use the quasi-harmonic approximation implemented in ptraj
> to calculate entropy and should not do any GB or PB calculations. I just
> tested this out with my AmberTools 1.5 version and it worked just fine.
>
> -Bill
>
>
>
> 2011/5/12 Jesper Sørensen <lists.jsx.dk>
>
> > Hi Bill,
> >
> > Thanks for the suggestions. I wanted to as a first rough estimate use
> > the entropy module in ptraj (through MMPBSA.py). Anyway to make that
> work?
> >
> > I haven't upgraded yet, but I will update it soon. I am currently
> > running AmberTools 1.4 with AMBER 11.
> >
> > Best,
> > Jesper
> >
> > -----Original Message-----
> > From: Bill Miller III [mailto:brmilleriii.gmail.com]
> > Sent: 12. maj 2011 12:55
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] MMPBSA.py - entropy only?
> >
> > This can definitely be done with MMPBSA.py. In fact, one of the test
> > cases for MMPBSA.py does only nmode calculations. When you tried
> > excluding the &gb and &pb flags did you also remember to include the
> > &nmode flag?
> >
> > The MMPBSA.py input file in
> > $AMBERHOME/AmberTools/test/mmpbsa_py/06_NAB_Nmode/ performs only an
> > nmode calculation.
> >
> > MMPBSA input file for running nmode calculation &general
> > keep_files=0, strip_mdcrd=0,
> > /
> > &nmode
> > nmode_igb=1, nmode_istrng=0.1,
> > /
> >
> > Also, if you are not using AmberTools 1.5, then I strongly urge you to
> > upgrade since MMPBSA.py has undergone many improvements since its
> > original release with Amber 11.
> >
> > I hope that helps.
> >
> > -Bill
> >
> > 2011/5/12 Jesper Sørensen <lists.jsx.dk>
> >
> > > Hi Amberlist,
> > >
> > > I am wondering if there is a way to get MMPBSA.py to ONLY calculate
> > > the entropy. I have in a separate calculation done the MM-PBSA
> > > calculations and now I am trying to get the entropy term included as
> > > well. It would be silly to have to do the entire calculation one
> > > more
> > time.
> > >
> > > I tried just not including either the &gb or &pb flags, but then it
> > > defaults to &gb with standard settings. Is there a way to prevent
> > > this?
> > >
> > > Best,
> > > Jesper
> > >
> > >
> > > _______________________________________________
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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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > 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
>
>
> _______________________________________________
> AMBER mailing list
> 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
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Received on Thu May 12 2011 - 08:00:03 PDT
