I have one complex with two ligand and a receptor,after running MD and then MMPBSA.py as follow: MMPBSA.py -O -i pbsa.in -o result.dat -sp complex.prmtop -cp free complex.prmtop -lp ligand.prmtop -rp receptor.prmtop -y *.mdcrd I got this error: PrmtopError: Complex natom != receptor natom + ligand natom Exiting. All files have been retained. I have one prmtop.file for both ligand as input of ligand Z. Khatti, Ph.D student of Physical Chemistry,
Department of Chemistry, Iran University of Science & Technology,Tehran, Iran
On Sunday, February 15, 2015 5:07 PM, Jason Swails <jason.swails.gmail.com> wrote:
On Sun, Feb 15, 2015 at 12:31 AM, zahra khatti <zkhatti2000.yahoo.com>
wrote:
> Dear amber users In my case, there are two similar ligand and a
> receptor.How could I obtain binding free energy between them with
> MMPBSA.py?Is there any option ?
Yes. Run MD simulations for both bound complexes and then run MMPBSA.py
on the result.
For more information, consult the tutorials at
http://ambermd.org/tutorials
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Feb 15 2015 - 07:00:02 PST
