AMBER Archive (2009)

Subject: Re: [AMBER] how to choose different comformations for RESP

From: cgji (
Date: Tue Jun 02 2009 - 00:14:02 CDT

hi, pang

 One paper of Duan Yong may helps .

T. Wang and Y. Duan (2007) "Chromophore Channeling in the G-Protein Coupled Receptor Rhodopsin", J. Am. Chem. Soc. (Communication), 129(22), 6970-6971

Please Check support information of this paper.


Chang G. JI
Institute of Theoretical and Computational Chemistry
Department of Chemistry
Nanjing University
Nanjing 210093



发件人: xueqin pang
发送时间: 2009-06-02 08:36:27
收件人: amber mail list; FyD
主题: [AMBER] how to choose different comformations for RESP
Hello everyone,

Thanks very much for your reply on the partial charge calculation of lipid membrane.

I intend to get the partial charges with RESP after optimization with Gauss. However the output of Gauss for the lipid (dppc) differs a lot from the input conformation which is one molecular of the pre-stabled lipid membrane (I intend to attach the file behind but failed).

So I want to ask: which file should I use in RESP, the input (one of the lipid molecular in a equilibrated lipid membrane) or the output (optimization of the input HF/6-31G*)?

What is more I get the partial charges of both the input and output confirmations of dppc with AM1-BCC, which is of cause a little different between them. Again I am wondering which one to use in my MD stimulation.
Thanks again

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
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