On Tue, Jul 21, 2015 at 12:55 AM, Ayesha Fatima <ayeshafatima.69.gmail.com>
wrote:
> Dear All,
> I have run 2ns qm/mm on a stabilised ligand-protein complex using AMBER12.
I want to calculate the free binding energy. First I used the mm_pbsa.pl
> using the script by Holger Gohlke. I modified the &GB section to include
> the qm parameters. The output returned positive values for GBTOT which are
> rather high.
> Then I tried to use the mmpbsa.py method and created the mmpbsa.in file as
> indicated on the mailing list. The mdins files were created and as
> mentioned on the mailing list to remove the "dec_verbose" and rerun the
> mmpbsa. I did that however the error of CalcError: sander failed with
> prmtop ../prot33.top! is coming.
> Can someone guide me to set up?
>
Do you get the same issue when you run with AmberTools 15? Amber 12 is
rather old at this point (released over 3 years ago), and there have been
numerous fixes and improvements to MMPBSA.py since then.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 21 2015 - 09:30:03 PDT
