Sorry, I didn't know that.
Sajeewa
On Fri, Oct 12, 2012 at 5:26 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> you would need to tell people how you generated the prmtop- what program,
> what version what is the molecule(s) involved, and so on.
>
>
> On Fri, Oct 12, 2012 at 5:23 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com
> >wrote:
>
> > ---------- Forwarded message ----------
> > From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
> > Date: Fri, Oct 12, 2012 at 2:24 PM
> > Subject: Notes and warnings in the generalized Born calculation
> > To: AMBER Mailing List <amber.ambermd.org>
> >
> >
> > Hi all,
> >
> > I go the following notes and warnings in the output files (mdout) for the
> > generalized Born MD calculations.
> >
> > Note: 1-4 EEL scale factors were NOT found in the topology file.
> > | Using default value of 1.2.
> >
> > I need a suggestion on how to have those 1-4 EEL scale factors in the
> > .prmtop file. Would it have a big effect if I leave it as it is (with
> > default value of 1.2)?
> >
> > | Note: 1-4 VDW scale factors were NOT found in the topology file.
> > | Using default value of 2.0.
> >
> > I need a suggestion on how to have those 1-4 VDW scale factors in the
> > .prmtop file. Would it have a big effect if I leave it as it is (with
> > default value of 2.0)?
> >
> >
> > | WARNING: ATOMIC_NUMBER section not found. Guessing atomic numbers from
> > | masses for GB parameters. Remake topology file with AmberTools
> > 12+
> > | or add atomic numbers with ParmEd to remove this warning.
> >
> > Here, I would really appreciate a suggestion on how to add atomic
> numbers
> > using ParmEd.
> >
> > Thank you
> >
> > Sajeewa Dewage
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Oct 12 2012 - 19:00:04 PDT
