[gmx-users] angle between helices

[Alan Dodd]

g_bundle does give the angle between helix pairs...?  Not directly, admittedly, but it gives you the tilt from the main axes, which you can use with some basic math to work out the angle between helices.

----- Original Message ----
From: Anupam Nath Jha <anupam at mbu.iisc.ernet.in>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, October 29, 2007 10:37:13 AM
Subject: Re: [gmx-users] angle between helices

HI David
there are options like g_helix, g_angle and as you said g_bundle, but none of
them gives the angle between helix pairs.

anupam


> Marc F. Lensink wrote:
>> On Mon, Oct 29, 2007 at 05:31:18PM +1100, Mark Abraham wrote:
>>> Anupam Nath Jha wrote:
>>>> Dear all
>>>> can i calculate the angle between trans-membrane alpha-helices by using
>>>> gromacs?
>>> Probably. Check out section 7.4 of the manual.
>>
>> i wrote a program for that.  contact me off-list.
>>
>> as soon as i find a free moment, i'll upload it to the contrib page.
>>
> otherwise g_bundle might do it
>
>> cheers,
>> marc
>>
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>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205. Fax: +4618511755.
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--
Science is facts; just as houses are made of stone, so is science is made of
facts; but a pile of stones is not a house, and  a collection of facts is not
necessarily science.

Anupam Nath Jha
Ph. D. Student
Saraswathi Vishveshwara Lab
Molecular Biophysics Unit
IISc,Bangalore-560012
Karnataka
Ph. no.-22932611



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