[AMBER] pH based conformational study

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Wed, 16 Jun 2010 12:25:18 +0530 (IST)

Hello all

I am doing pH based conformational study.

I have prepared CPIN file there is by default protonation state is 0 for side chain
of titratable residues.During generation of this file I havent specify the
protonation state.

Should I modifify the protonation state before doing MD simulation or I can
If is it so then why?

Whatever I got from manual that during Md simulation diffrent ptonation state is
sample out by each MC sampling step.

So should I left initial protonation state 0 or chang it.
Can anybody please explain this.

With regard
Sangita Kachhap

AMBER mailing list
Received on Wed Jun 16 2010 - 00:00:03 PDT
Custom Search