Re: [AMBER] cpptraj GIST

From: Daniel Roe <>
Date: Fri, 26 May 2017 13:54:29 -0400


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.


On Fri, May 26, 2017 at 1:49 PM, Gabriel Jara
<> 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 Química / UNICAMP
> Rua Josué de Castro s/n
> Cidade Universitária "Zeferino Vaz", Barão Geraldo
> 13083-861 Campinas, São Paulo, Brasil
> ------
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Fri May 26 2017 - 11:00:03 PDT
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