AMBER Archive (2009)

Subject: Re: [AMBER] GLYCAM: warnings by writing topology

From: Karl Kirschner (kkirsch_at_scai.fraunhofer.de)
Date: Wed Jun 17 2009 - 03:33:55 CDT

Hi Sergey,

> However, CG in leaprc.ff03 is sp2-hybridized. Could it be that when I

You are right, that CG is labled as an sp2-hybridized atom. However, I checked
frcmod.ff03 does not have any CG atom type (same is true for parm99.dat,
which is loaded with ff03). So, I am not sure why this is included in
leaprc.ff03. Maybe someone else can comment who knows better.

When we developed Glycam_06, we designated sp3 carbons as CG to distinguish it
from the other force fields - meaning that almost all of the Glycam torsion
angles contain a CG atom type, so when it is loaded with a protein force
field there is no overwriting of the protein torsion parameters.

As a test, if CG is truely not needed by ff03 or parm99, then try deleting it
from the leaprc.ff03 file and see what happens.

Cheers,
Karl

P.S. I checked leaprc.ff99SB, and CG also exist there as sp2, but I don't
think the force field uses that atom type. Can anyone else comment?

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