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
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Received on Thu May 12 2011 - 04:30:03 PDT
