Re: [AMBER] MD simulation of a protein at pH 3.0

From: Rakesh Srivastava <allahabad.21.gmail.com>
Date: Sat, 17 Feb 2018 10:16:16 +0530

Thanks Vinícius Wilian D Cruzeiro for your kind reply.

Rakesh Srivastava
Research Fellow
School of Computational & Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067
India


On Fri, Feb 16, 2018 at 7:31 PM, Cruzeiro,Vinicius Wilian D <
vwcruzeiro.ufl.edu> wrote:

> 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 - 21:00:03 PST