On Fri, 2014-04-04 at 15:30 +0530, Souvik Sur wrote:
> Dear Amber users,
> I have a problem regarding calculation using MMPBSA.py script.The
> script can not recognize the receptor and ligand separately as I have
> written ...
> =========================================================================== MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp souvik_fixed.prmtop -cp 22-aro-ant.prmtop -rp 22-ant.prmtop -lp aro-ant.prmtop -y *.mdcrd
> Error :PrmtopError : Complex nres ! = receptor nres + ligand
> nresExiting. All files have been
> retained.====================================================================================================
> How can I solve it, means I want to know how can I modify my .prmtop
> file for recognizing complex, receptor and ligand separately at this
> stage.
This means that the number of residues in your receptor and ligand
topology files is not equal to the number of residues in your complex
topology file. This is a fundamental requirement behind the theory of
MM/PBSA and indicates that your setup procedure in which you generated
the topology files is flawed.
The names of your files suggests that whatever the "ant" species is is
present in the complex, receptor, and ligand topologies. Every residue
in the complex must be in either the receptor OR ligand, but never both.
If you continue having troubles, I suggest working through the tutorials
(using the system provided there as an example first) and then switching
to your system after you finished the example successfully and have a
good technical understanding of what is being done behind the scenes at
each step. Using MMPBSA.py (or any MM/PBSA script) as a black box is
strongly discouraged.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 04 2014 - 05:00:02 PDT
