These are questions that you should ask the amber reflector:
amber.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
>
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NOTE NEW MAILING ADDRESS & FAX NUMBER:
James W. Caldwell (voice) 415-476-8603
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University of California
San Francisco, CA 94143-2240
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Received on Tue May 20 2003 - 17:53:01 PDT
