AMBER Archive (2009)

Subject: [AMBER] partial charges of lipid membrane for GPCR system

From: xueqin pang (pangxueqintea_at_yahoo.com.cn)
Date: Tue May 26 2009 - 08:34:34 CDT

Hello every,
 
I am doing computational stimulation on GPCR with Amber10 now, and have the following problems when adding lipid membrane into the system.
 
1. Someone have treat the partial charges of CH3 and CH2 as 0, can we do the same thing in Amber. (J. Phys. Chem. B, Vol. 108, No. 14, 2004)
 
2. Someone do it as follows :"General Amber force field (GAFF) parameters were assigned to ligands and DPPC molecules, while the partial charges were calculated using the AM1-BCC method as implemented in the Antechamber suite of AMBER 8." Is the result reliable? (Journal of Medicinal Chemistry, 2006, Vol. 49, No. 14)
 
3. Can I get my topolygy of dppc with Antechember (GAFF), and then get the partial charges with RESP after optimization with Gauss?
 
Thanks a lot
 
===================================================================================================
 Pang Xueqin
 State Key Laboratory of Molecular Reaction Dynamics
 Dalian Institute of Chemical Physics
 Chinese Academy of Sciences.
 Tel: +86-411-84379352 Fax: +86-411-84675584
 http://www.english.dicp.ac.cn/
===================================================================================================

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