AMBER Archive (2003)

Subject: Re: From Dr. Ekaterina Nikitina

From: caldwell_at_heimdal.compchem.ucsf.edu
Date: Tue May 20 2003 - 11:27:04 CDT

These are questions that you should ask the amber reflector:
amber_at_heimdal.ucsf.edu

I will add your name to the subsctiption list.

jim

On Tue, 20 May 2003, Nikitina Ekaterina wrote:

> Dear Prof. James W. Caldwell,
> Some times ago my group (Institute of Applied Mechanics, Russian
> Academy of Science) has got licensed copy of Amber 7 from your side.
> Within the calculations in Amber I was faced with a problem that I can
> not calculate in MD the protein - ligand complexes in a solvent.
> Unfortunately I have not found in Amber Manual some clear explanation
> how to create input file *.prepin with parameters gaff for the ligand
> component and with parameters ff99 for the protein component of the
> complex and to calculate both components together as adsorption
> complex. Using Antechamber I can create *.prepin file for the ligand,
> and after that to put it to xleap, but how to calculate after that the
> protein – ligand complex I do not clearly understand.
> Would you or your colleagues be so kind to explain me how to solve
> this problem?
> Thank you in advance,
> Best regards,
> Dr. Ekaterina Nikitina
>
> ___________________
> Лучшие туры на ближайшие даты. Сеть магазинов горящих путевок.
> www.tournews.ru
> 

-- 

----------------------------------------------------------------------------
NOTE NEW MAILING ADDRESS & FAX NUMBER:

James W. Caldwell                         (voice) 415-476-8603
Department of Pharmaceutical Chemistry    (fax)   415-514-3866  
UCSF Box 2240                             (email) caldwell_at_heimdal.ucsf.edu
600 16th Street
University of California
San Francisco, CA 94143-2240
----------------------------------------------------------------------------