On Tue, Jun 25, 2013 at 12:37 PM, <eneas.usal.es> wrote:
>
> Hi everyone,
>
> Im trying to run an mmpbsa calculations with the python script. I have
> installed AmberTools 13.
>
> First, i read the tutorial from the webpage.
>
> I have my prmtop file and with cpptraj I created 3 prmtop files: complex,
> receptor and ligand (all without solvent or ions). The original one has
> both the solvan and ions.
>
> When i try to run the script, tne next message appears:
>
> mmpbsa -O -i pbsa.in -cp Acom.prmtop -rp Amac.prmtop -lp Alig.prmtop -y
> eq01.dcd
> Loading and checking parameter files for compatibility...
> PrmtopError: Inconsistent charge definition for atom 3399!
> Exiting. All files have been retained.
>
> I have opened the receptor and the complex prmtop files and check what was
> the chatge of that atom. Surprinsingly, it was the same!
>
Your error was quite weird. You have two residues named MOL in your
complex topology file which are actually _different_ residues, and
MMPBSA.py happens to assume that the ligand should be the 'first' one
rather than the second.
I'm not sure how you built the prmtop in the first place with two
identically-named units in leap, but this is one case where you will have
to specify the receptor and ligand masks manually in the MMPBSA input file.
So add the following variables to the &general section:
receptor_mask=:1-226, ligand_mask=:227
In general, you should try to give each ligand different residue names
(that will avoid this issue).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jun 25 2013 - 11:00:03 PDT
