Re: [AMBER] CpHMD: seeking clarification

From: Eric Lang <eric.lang.bristol.ac.uk>
Date: Mon, 25 Sep 2017 10:29:50 +0000

Hi George,


This is not surprising as using CpHMD all the Glu and Asp residues chosen to be titrable will become neutral and the His residues will become positively charged (You have probably renamed them AS4, GL4 and HIP in your PDB). This is explained in the Mongan paper for example.


Cheers,


Eric 


--
Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Adrian Mulholland's Research Group
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
________________________________
From: George Tzotzos <gtzotzos.me.com>
Sent: 24 September 2017 18:41
To: AMBER Mailing List
Subject: [AMBER] CpHMD: seeking clarification
Setting up two distinct simulations (a) conventional MD and (b) CpHMD for and identical solute using parameters for EWALD and TIP3P water, the unperturbed charges of the units were:
 -9 when using the ff14SB force field (conventional MD) and
 -1 when using leaprc.constph (CpHMD)
As my experience with CpHMD is rather limited, I’d be grateful for any clarifications on this issue
Many thanks in advance
George
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Received on Mon Sep 25 2017 - 04:00:02 PDT
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