Dear Ian,
Thank you very much!
I will try your student DMSO box. This is very helpful.
Thanks!
Best,
Yoel
Yoel Rodríguez, Ph.D.
CUNY / MSSM
________________________________
From: Gould, Ian R <i.gould.imperial.ac.uk>
Sent: Tuesday, July 2, 2019 4:23:24 AM
To: AMBER Mailing List
Subject: Re: [AMBER] MD Simulation in DMSO
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.
https://urldefense.proofpoint.com/v2/url?u=http-3A__research.bmh.manchester.ac.uk_bryce_amber&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=hVgs2MTRFepPtJy5rTN5kTyTBgyQpf_ydrz5RjxxmQs&m=dKk40uMdmfovEu_vaLLQODA1fVYyqRdPQO3Vutgx9qs&s=R34E3pkK7sqT69MTM3sAi3HXMU17CaSFFxi5EJPI1yA&e=
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
https://urldefense.proofpoint.com/v2/url?u=http-3A__www3.imperial.ac.uk_people_i.gould&d=DwIGaQ&c=shNJtf5dKgNcPZ6Yh64b-A&r=hVgs2MTRFepPtJy5rTN5kTyTBgyQpf_ydrz5RjxxmQs&m=dKk40uMdmfovEu_vaLLQODA1fVYyqRdPQO3Vutgx9qs&s=4sa4XRip7QUuT93icXgktbz9Rfkc7uzbDGsYrebWZlk&e=
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 - 12:00:02 PDT
