Re: [AMBER] Fwd: Notes and warnings in the generalized Born calculation

From: David A Case <>
Date: Fri, 12 Oct 2012 20:48:35 -0400

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.


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Received on Fri Oct 12 2012 - 18:00:03 PDT
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