Hi Zhonghua,
Do you mean that I should delete one SAM from the complex file and then generate parameter file? and similarly do it for other ligand?
with regards,
Abhishek
________________________________
From: Xia, Zhonghua <zhonghua.xia.helmholtz-muenchen.de>
Sent: Tuesday, June 18, 2019 2:19 PM
To: AMBER Mailing List
Subject: Re: [AMBER] MM-PBSA
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
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Received on Tue Jun 18 2019 - 12:00:02 PDT
