This really helps. Thank you very much.
Sajeewa
On Fri, Oct 12, 2012 at 8:48 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Fri, Oct 12, 2012, Sajeewa Pemasinghe wrote:
> >
> > 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)?
>
> You don't need to have the 1-4 scaling factors in the prmtop file *unless*
> you want to use different scale factors for different torsions. The main
> (but
> not only) place this comes up is when mixing GLYCAM and protein force
> fields.
>
> Of course, we do recommend that people update to the current version of
> AmberTools, which will put these scale factors in the prmtop file. But old
> prmtop files that you created before are probably fine.
>
> >
> > | 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.
>
> Again, in most cases there is no need to change existing prmtop files. The
> only time you need atomic numbers is if you have non-standard residues with
> strange atom names, such that the programs would make a mistake in guessing
> what type of atom you have based on its name.
>
> ...dac
>
>
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Received on Fri Oct 12 2012 - 19:00:03 PDT
