AMBER Archive (2003)

Subject: Re: VdW in FEP

From: ENikitina (enikitina1_at_yandex.ru)
Date: Tue Jun 10 2003 - 06:56:23 CDT

Thank you very much for your valuable help.

Dr. E. Nikitina

>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
>
>--
>
>==================================================================
>David A. Case | e-mail: case_at_scripps.edu
>Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
>The Scripps Research Institute | phone: +1-858-784-9768
>10550 N. Torrey Pines Rd. | home page:
>La Jolla CA 92037 USA | http://www.scripps.edu/case
>==================================================================
>