Re: [AMBER] MM-PBSA

From: Xia, Zhonghua <zhonghua.xia.helmholtz-muenchen.de>
Date: Tue, 18 Jun 2019 20:19:43 +0200 (CEST)

Hi,

Maybe generate and provide the ligand parameter file separately. And then run MMPBSA.py twice.

Best,
Zhonghua

----- 原始邮件 -----
发件人: "Thakur, Abhishek" <axt651.miami.edu>
收件人: amber.ambermd.org
发送时间: 星期二, 2019年 6 月 18日 下午 8:09:07
主题: [AMBER] MM-PBSA

Hi everyone,

I have a small doubt regarding MM-PBSA.

I have carried out 1000ns simulation for a dimer and on both dimeric unit I have a ligand SAM (residue number 301 and 602). Is there any way that I can carry out the MM-PBSA for both ligand separately?
As of now after computing the binding energy it is not clear that result is for SAM 301 or 602.

Any suggestion will be highly appreciated.


with regards,
Abhishek

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-- 
Zhonghua XIA • Doctoral Student
Institute of Structural Biology
Helmholtz Zentrum Muenchen
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Received on Tue Jun 18 2019 - 11:30:03 PDT