AMBER Archive (2006)

Subject: AMBER: GPCR-membrane issue

From: Akshay Patny (
Date: Wed Sep 20 2006 - 12:30:24 CDT

Hi All


I have been trying to set up a system for GPCR-Ligand simulation in
Membrane-Aqueous environment.


Without the non-standard residue (Antagonist), I have been able to
successfully setup the system including: Protein, Membrane (POPC generated
by VMD), Water, and Ions using VMD scripts and the CHARMM topology file
top_all27_protein_lipid.inp present in VMD.


Now following is my problem:


1. I want to do the MD simulation using AMBER 8/9. I am planning to use
the GAFF parameters for the Ligand, Lipids, Waters, and Ions; and FF99/FF03
for the Protein part. My question is: If I prepare a PDB (and a
corresponding PSF) of the entire system using VMD which uses CHARMM topology
file top_all27_protein_lipid.inp. Would I then be able to use this PDB file
to create corresponding INPCRD and PRMTOP files for simulation applying GAFF
and FF09/FF03 parameters in LEAP module in AMBER?


Thanks a lot.

Akshay Patny

Graduate Research Assistant
Faser Hall 417, Department of Medicinal Chemistry

Research Institute of Pharmaceutical Sciences
University of Mississippi
University, MS 38677
Tel: 662-915-1286 (office); Web:


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