AMBER Archive (2005)

Subject: Re: AMBER: Which source file determine the initial value of IX XX arrray in AMBER8?

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Sat May 14 2005 - 12:52:56 CDT

look at rdparm.f, and also look at the amber web page where
the prmtop format is given in detail.

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

caoch_at_cherry.bio.titech.ac.jp wrote:

>hello:
>
> i want to add a new energy potential(12-3 form VDW) to the system in
>AMBER8. i tried to understand how AMBER gets system's energy and force.
>In the 'subroutine bond 'it seems AMBER uses the information from several
>array such as IX XX IB JB to caculate energy and force.
> I guess these array get values from topology file but I don not know
>which source file does this work.
> I am not very simlar with AMBER and I will be very appreciated for any
>advice.
>
> caoch
> BIO. Center Tokyo Institute of Technology
>
>

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