Re: [AMBER] generating topology without loading Frcmod file

From: Arun Srikanth <askforarun.gmail.com>
Date: Wed, 24 Jun 2015 18:13:00 -0400

The problem occurs with one of the molecule (in the mixture). So I
investigated this molecule separately.

So for this molecule the total number of dihedrals 102.

For two molecules (same molecule) the total number of dihedrals is 205.

I am attaching the pdb files respectively.

Please let me know as why there is an extra dihedral in topology file.

Is this a bug ?

Thanks
Arun





On Wed, Jun 24, 2015 at 5:26 PM, Jason Swails <jason.swails.gmail.com>
wrote:

> On Wed, Jun 24, 2015 at 4:45 PM, Arun Srikanth <askforarun.gmail.com>
> wrote:
>
> > Thanks. I have another question now.
> >
> > I am preparing a mixture of two molecules in the ratio of 3:2.
> > I have the individual topology files of the molecules from tleap.
> > I have also generated the topology file for the mixture(3:2) from tleap
> > The number of dihedrals for the mixture is 685 (including impropers). The
> > individual number of dihedrals are 160 and 102 for each of the molecules.
> > Now for 3:2 ratio the total number of dihedrals should be 684 (3x160
> > +2x102). However I am getting one dihedral extra from the topology file
> of
> > the mixture.
> >
> > Why is this so ?
> >
>
> ​No clue. Any idea *what* the extra dihedral term is?​ If not, can you
> send me the relevant files to try and reproduce this?
>
> Thanks,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Wed Jun 24 2015 - 15:30:02 PDT
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