AMBER Archive (2003)

Subject: Re: From Dr. Ekaterina Nikitina

From: David A. Case (case_at_scripps.edu)
Date: Thu May 22 2003 - 12:16:58 CDT

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?

Basically, you are most of the way there. You need to create a pdb file
with an initial model of your complex. Put a "TER" card between the protein
and ligand. Then, load your ligand prepin file, followed by the PDB file.
LEaP should recognize everything in the pdb file (work to fix this if it
doesn't). You can then procede to solvate (or whatever) just as for a
protein by itself.

If this doesn't answer your question, you need to ask a more specific one.

..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
The Scripps Research Institute    |  phone:        +1-858-784-9768
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