Dear Yoel,
Many years ago a graduate student of mine, John Dalmaris created a DMSO box of solvent based on the work of Tom Fox and Peter Kollman. The parameters for the DMSO unit were taken from: Thomas Fox and Peter A. Kollman (J. Phys. Chem. B., 1998, 102, 8070-8079) . He ran explicit simulations of peptides and proteins in it. The box and frcmod etc are on Richard Bryce's website.
http://research.bmh.manchester.ac.uk/bryce/amber
HTH
Ian
Tyrell: I'm surprised you didn't come here sooner.
Roy: It's not an easy thing to meet your maker.
Tyrell: What could he do for you?
Roy: Can the maker repair what he makes?
Bladerunner
--
Professor Ian R Gould, FRSC.
Professor of Computational Chemical Biology
Department of Chemistry
Imperial College London
Exhibition Road
London
SW7 2AY
E-mail i.gould.imperial.ac.uk
http://www3.imperial.ac.uk/people/i.gould
Tel +44 (0)207 594 5809
On 02/07/2019, 09:16, "Rodriguez, Yoel" <yoel.rodriguez.mssm.edu> wrote:
Hello Amber community,
I am reaching out to you because I would like to run an MD simulation in DMSO. The system is formed by a small peptide of 4 amino acids bound to small molecule.
Does someone have experience running MD simulation in DMSO? Any suggestion using implicit model to mimic DMSO as a solvent.
Feedback is really appreciated.
Thank you in advance.
Best,
Yoel
Yoel Rodríguez, Ph.D.
CUNY / MSSM
________________________________
From: Rodriguez, Yoel
Sent: Monday, June 24, 2019 8:11:53 AM
To: AMBER Mailing List
Subject: MD Simulation in DMSO
Hello Amber community,
I am reaching out to you because I would like to run an MD simulation in DMSO. The system is formed by a small peptide of 4 amino acids bound to small molecule.
Does someone have experience running MD simulation in DMSO? Any suggestion using implicit model to mimic DMSO as a solvent.
Feedback is really appreciated.
Thank you in advance.
Best,
Yoel
Yoel Rodríguez, Ph.D.
CUNY / MSSM
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Received on Tue Jul 02 2019 - 01:30:02 PDT
