Re: [AMBER] Suggestions for Analysis

From: dhaval patel <>
Date: Wed, 20 Feb 2019 10:19:58 +0530

Dear Souvik,
There is a number of things one can do with any MD packages. Refer few
pieces of literature related to your kind of work and you will get all the
info for the same. One important thing I would like to ask you is which
force-field you used for simulations of intrinsically disordered proteins?

Sincerely yours,
Dhaval Patel | PhD
The M. S. University of Baroda, Vadodara.
Lab: Biophysics & Structural Biology,
Indian Institute of Advanced Research,
Gujarat, INDIA. +91 9925450504;

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On Wed, Feb 20, 2019 at 5:20 AM Souvik Dey <> wrote:

> Dear Amber users,
> First of all this may not be a proper platform to ask this question. Sorry
> if you find this inappropriate.
> I am simulating an intrinsically disordered protein in Amber to extract
> some structural information and later plan to simulate the same protein in
> presence of a membrane to find out any possible structural modifications.
> Since I am very new to this field, I was wondering if someone could tell me
> about what possible analysis may I carry out in Amber. So, far I have
> calculated the radius of gyration and DSSP.
> Thanks in advance.
> Souvik
> ----------------------------------------------------------
> Souvik Dey
> Graduate Student
> Department of Chemistry
> University of Illinois Chicago
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Received on Tue Feb 19 2019 - 21:00:02 PST
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