Re: GBIS synamics

From: David Tanner (guacamoleo_at_gmail.com)
Date: Wed Mar 02 2011 - 07:56:59 CST

1) NAMD GBIS does not have a SASA term.
2) NAMD internally loads a certain set of radii, which corresponds to
"PBradii bondi", users cannot change this.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
David E. Tanner
Theoretical and Computational Biophysics Group
3159 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801
http://www.linkedin.com/in/davidetanner
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On Mar 2, 2011, at 5:02 AM, Francesco Oteri wrote:

Dear NAMD users,
I'd run a Generalized Born Implicit Solvent MD with AMBER force-field.
I've two question related to the method:

1) In the AMBER user manual where this method is described, it is
cited a Solvent Accessible Surface dependent term, but I don't find
any related term in the NAMD user guide. How is treated this term?

2) In the AMBER manual, the authors say:

     With this option, you should use the LEaP command "set default
PBradii mbondi2" or "set default PBradii bondi" to prepare the prmtop
file

     Is It true for NAMD?

     Thanks,

                                                                                                                                                         Francesco

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