Hi Jason & Bill,
Just to clarify, i meant the setting "strip_mdcrd=0" and I guess calling
that a "flag" is wrong - sorry :-)
If I run an entropy calculation using the following input:
&general
interval=1000,verbose=2,entropy=1
/
I get the entropy calculation, but also the MM/GBSA results... in the end of
my FINAL_RESULTS_MMPBSA.dat it says:
Warning: No calculation namelist flags specified! Assuming GB with default
values. This is for Ambertools 1.4 and amber 11, so perhaps this has changed
to ambertools 1.5.
Best,
Jesper
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: 13. maj 2011 01:07
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA.py - entropy only?
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.
>
Since there's nothing of substance to add to Bill's analysis (which is
completely right), I'll simply add the useless "there's no such thing as the
mdcrd=0 flag" comment. You can supply trajectory files on the command-line,
and there are some input variables that have mdcrd in them (i.e.
strip_mdcrd), but mdcrd=0 should raise an error wherever it's placed in
MMPBSA.py...
What flag are you referring to? Also, if you don't do entropy=1, then it
will do a GB calculation by default if no other calculation namelist is
present (i.e. &pb, &rism, or &nmode; &alanine_scanning and &decomp are not
in themselves a solvent model and will therefore invoke a GB approximation
by default).
HTH (but it's unlikely),
Jason
> 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
> > >
> > >
> > > _______________________________________________
> > > 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
> _______________________________________________
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 13 2011 - 04:00:02 PDT
