Thanks a lot
Emilio
> Date: Fri, 14 Nov 2014 07:59:56 -0500
> From: case.biomaps.rutgers.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] minimization problema
>
> 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 - 07:00:02 PST
