AMBER Archive (2008)

Subject: Re: AMBER: MOIL-View is for SGI. How do we analyze LES trajectories?

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sat Aug 23 2008 - 07:39:16 CDT

this should work in ptraj- if not then contact me off the amber list,
I have a small program that will do this.
try ptraj first, though, it has more features and my program has no
documentation.

On Wed, Aug 20, 2008 at 6:42 PM, Sasha Buzko <obuzko_at_ucla.edu> wrote:
> As a follow up to my earlier question.
>
> Since MOIL-View site is down (and even when it's up, MOIL-View is for SGI
> only), how do we analyze LES results?
>
> AMBER manual doesn't contain any suggestions for LES analysis, other then
> reference to MOIL-View. Are there any alternatives?
>
> Thanks very much for any suggestions
>
> Sasha
>
>
> Sasha Buzko wrote:
>
> Carlos,
> the book with the command line claim: "Molecular modeling of proteins"
> edited by Andreas Kukol, ISBN 978-1-58829-864-5. The reference is on page
> 267 (chapter V).
>
> In the meantime, could you suggest other ways to deal with the LES data?
> Thanks
>
> Sasha
>
>
> Carlos Simmerling wrote:
>
> no there is not a command line version. web site should be up soon,
> just changed servers. not sure what that article meant, can you give
> full ref?
>
> On 8/20/08, Sasha Buzko <obuzko_at_ucla.edu> wrote:
>
>
> Hi,
> We are looking for ways to analyze LES results, and MOIL-View appears to
> be available only for SGI. On the other hand, "Molecular modeling of
> proteins" edited by Kukol (2008) claims on page 267 that there is a
> command line version that can run under Linux. Is it correct?
> If so, how can I get hold of it? If not, are there any alternatives?
> The original MOIL-View web site seems to be out of maintenance, and no
> recent information is available.
>
> Thanks for any hints
>
> Sasha
>
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
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Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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