Dear Prof. Kurtzman,
Sorry for th delay.
I am looking for an implentation of the actual code on my system, which
solvent is chloroform.
I am interested in writing a code to include chloroform (and generalize to
other organic solvents). However, at the moment, I must finish my posdoc
and I am searching for a new position. Later, I would like to write a code
and I would like to write to you for help.
Thank you for answer and help.
Gabriel
Message: 14
Date: Wed, 31 May 2017 08:52:27 -0400
From: Tom Kurtzman <simpleliquid.gmail.com>
Subject: Re: [AMBER] cpptraj GIST
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
<CA+Fivs4RRjnU257fUPXPiKZDoBgkT0w-_PtmCW3jam6tuaJP3A.mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"
This came up in my group a couple of weeks ago with regards to methanol.
Depending on whether our grant gets renewed, we will or won't be working on
developing the code for rigid solvents starting in the Fall.
Gabriel, if you are interested in writing some code, my lab can help guide
you through it. It is straightforward but the coding may be tricky
especially if it is generalized to all rigid solutes.
Tom
On Fri, May 26, 2017 at 1:54 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> GIST can be generalized to other solvents but it has not been, at
> least not in cpptraj. This would require some extra coding to get
> working and I'm not sure when that would happen. So unfortunately
> cpptraj can not do what you want yet.
>
> -Dan
>
> On Fri, May 26, 2017 at 1:49 PM, Gabriel Jara
> <gabriel.fcq.unc.ar.gmail.com> wrote:
> > Dear all,
> >
> > I would like to perform solvent calculations over a peptide solvated by
> > chloroform. I red amber manual and there is a tool called GIST for
> > analyzing the structure and thermodynamics of solvent in the vicinity of
> a
> > solute molecule. Also, in the manual is specified that "The current
> > implementation works for only water, but the method can be generalized
to
> > other solvents whose molecules are rigid like water, such as chloroform
> or
> > dimethyl-
> > sulfoxide (DMSO)." The tutorial specifies that the implementation is for
> > water models only. However, my question is possible to apply that
> > generalization to analyze chloroform structure and thermodynamics?
> >
> > Thanks in advance.
> >
> > Gabriel
> >
> > --
> > Dr. Gabriel E. Jara
> > Instituto de Qu?mica / UNICAMP
> > Rua Josu? de Castro s/n
> > Cidade Universit?ria "Zeferino Vaz", Bar?o Geraldo
> > 13083-861 Campinas, S?o Paulo, Brasil
> > ------
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
************************************************
Tom Kurtzman, Ph.D.
Assistant Professor
Department of Chemistry
Lehman College, CUNY
250 Bedford Park Blvd. West
Bronx, New York 10468
718-960-8832
http://www.lehman.edu/faculty/tkurtzman/
<http://www.lehman.edu/faculty/tkurtzman/index.html>
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Received on Mon Jun 05 2017 - 11:30:03 PDT
