On Thu, Nov 13, 2014, Emilio Angelina wrote:
>
> I am running a minimization of a haloperidol-like compound in a cubic
> box o waters. After a small number o minimization cycles, the ligand
> breaks into several parts. I guess that the problem might be in the
> definition of bonds/angles/dihedrals in the topology file. However, it
> is hard for me to find where exactly is the problem.
I'd suggest using parmed.py to examine the list of bonds in your prmtop file.
If the ligand breaks into several parts, there are probably some missing
bonds.
Looking at the prmtop file should give some clues, but (assuming this is
indeed the problem), the error arose in creating the library file (usually
in prepin or mol2 format, and I recommend mol2.) You can also look at the
list of bonds in that file.
If there is a problem with the mol2 file, then you have to go back one more
step to think about how you created that file. (Antechamber? R.E.D.?
something else?)
...good luck...dac
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Received on Fri Nov 14 2014 - 05:30:02 PST
