Hello Rakesh,
AMBER has an option (icnstph=2) that let's you do the MD steps in explicit solvent and the protonation state change attempts in implicit solvent. Jason Swails wrote a tutorial about it: http://jswails.wikidot.com/explicit-solvent-constant-ph-md
The cpinutils.py tool let's you choose which residues to titrate. At pH 3 one would expect the aspartate and glutamate residues to be the most relevant ones, but you can run a short simulation letting a large number of residues titrate and check which ones are relevant for your specific system at the pH you want. Then select only these for your production simulations.
I hope this helps,
Best,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Rakesh Srivastava <allahabad.21.gmail.com>
Sent: Friday, February 16, 2018 7:15:48 AM
To: AMBER Mailing List
Subject: [AMBER] MD simulation of a protein at pH 3.0
Hello all,
I want to go for MD simulation of a protein at pH 3.0. I went through the
tutorial and it says to change some residue names but I do not understand
how to decide which are my titrable groups needed to be edited and which to
be not. Further the method cphmd uses implicit solvent method. Is there any
option for running MD simulation at pH 3.0 with explicit solvent model ?
Any help will be appreciated.
Thanks.
Rakesh Srivastava
Research Fellow
School of Computational & Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067
India
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Received on Fri Feb 16 2018 - 06:30:02 PST
