AMBER Archive (2008)

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

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Sat Aug 23 2008 - 15:19:07 CDT

Thanks, Carlos.
Will tray ptraj.

Sasha

Carlos Simmerling wrote:
> 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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>
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>

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