AMBER Archive (2003)

Subject: Re: VdW in FEP

From: David A. Case (case_at_scripps.edu)
Date: Mon Jun 09 2003 - 10:05:58 CDT

On Mon, Jun 09, 2003, ENikitina wrote:
>
> I?m running some free energy calculations with Gibbs (FEP) and I face
> problem with non-electrostatic contribution calculation. Can you help me to
> define the van-der-Waals parameters in perturbated molecule (I haven?t found
> such option in xLEaP)?

van der Waals parameters are based on the atom type; so you must define the
peturbed atom type in LEaP in order to get the vdW parameters you want.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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