Re: [AMBER] Constant pH simulation of PyroPhosphate in Explicit solvent

From: Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>
Date: Mon, 17 Jun 2019 17:52:03 +0000

Hello Yuvraj,

Did you take a look at the constant pH tutorials as well? If not, here are the links:

http://ambermd.org/tutorials/advanced/tutorial18/index.htm

http://jswails.wikidot.com/explicit-solvent-constant-ph-md

Best,


Vinícius Wilian D. Cruzeiro

PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States

Voice: +1(352)846-1633

________________________________
From: Yuvraj Singh <ys3382.nyu.edu>
Sent: Monday, June 17, 2019 11:58 AM
To: amber.ambermd.org
Subject: [AMBER] Constant pH simulation of PyroPhosphate in Explicit solvent

Dear All,

I am trying to simulate a single Pyrophosphate molecule in TIP3P water
under a constant pH (like 7). I read through the manual I understand how
it's done for different peptides, I'm just not sure how to begin with this
particular molecule.
Thank you,

Yuvraj
Yuvraj Singh
Hocky Research Group
Department of Chemistry
New York University
https://urldefense.proofpoint.com/v2/url?u=http-3A__hockygroup.hosting.nyu.edu_&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=vg8iTdivJL1PEwCvcH8P2DFF-Rtc9lAQvIqnaSWm1Pc&m=P8Fse49eqpdz4eNQxnXrkTVmlIihqZEcFaJOZeRSU08&s=sgC0F-hQWAO3RY3FpOUJgKiG0C56RJCBSTb2nSX8VW4&e=
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Received on Mon Jun 17 2019 - 11:00:02 PDT
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