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