Hi Dan,
Thank you for your explanation.
Gabriel
> Message: 10
> Date: Fri, 26 May 2017 13:54:29 -0400
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] cpptraj GIST
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qObq3o=qwicz+DNCymQKFEfQcSdackanqUK-0Oy0q0=
> 3Tw.mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> 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
> > ------
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> > 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
>
>
>
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> End of AMBER Digest, Vol 1946, Issue 1
> **************************************
>
--
Dr. Gabriel E. Jara
Instituto de Química / UNICAMP
Rua Josué de Castro s/n
Cidade Universitária "Zeferino Vaz", Barão Geraldo
13083-861 Campinas, São Paulo, Brasil
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Received on Mon Jun 05 2017 - 09:00:02 PDT
