This really helps. Thank you very much.
Sajeewa
On Fri, Oct 12, 2012 at 8:12 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, Oct 12, 2012 at 8:24 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com
> >wrote:
>
> > 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)?
> >
>
> If you have sugar groups (or anything parametrized with GLYCAM), you will
> need to regenerate your prmtop with tleap from AmberTools 12. Otherwise,
> this is the correct default.
>
>
> >
> > | 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)?
> >
>
> Same answer as above. 2.0 is the 'correct' value for the Amber force
> fields.
>
>
> >
> >
> > | 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.
> >
>
> Open your prmtop in xparmed.py. Click "addAtomicNumber". Click "yes".
> Click "Write new prmtop".
>
> Unless you modified the atomic masses in your prmtop, though, this is
> unnecessary.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Fri Oct 12 2012 - 19:00:02 PDT
