AMBER Archive (2008)

Subject: RE: AMBER: Location of vdw radii and partial charges for ff99SB

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Sep 29 2008 - 09:51:44 CDT

See $AMBERHOME/dat/leap/parm/parm99.dat

 

This lists all the parameters for the atom types (bonds, angles, dihedrals
and VDW params) - the only difference for FF99SB is that it changes some of
the backbone parameters as specified in frcmod.ff99SB.

 

The charges and atom types are in

 

$AMBERHOME/dat/leap/lib/all_amino94.lib / all_aminoct94.lib /
all_aminont94.lib

 

You can also look at these visually in xleap with:

 

source leaprc.ff99SB

edit GLY

 

and then in the Display menu you can turn on the display of charges, atom
types etc.

 

Good luck,

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Charles Letner, Ph.D.
Sent: Monday, September 29, 2008 6:08 AM
To: amber_at_scripps.edu
Subject: AMBER: Location of vdw radii and partial charges for ff99SB

 

 

Hello,

Is there a file (or two) that lists the vdw radii and partial charges for
each amino acid atom type for the ff99SB. I am looking for both charged and
uncharged amino acids and n/co-terminal parameters. I am looking for a file
(or two) that is easy to "read".

 

Cheers,

Chuck

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