[gmx-users] Dihedral restraints

[Behnoush Zare]

Thank you Justin. I tried with g_angle and it worked.It gave me some .xvg files such as angdist.xvg , angaver.xvg ,dihfrac.xvg ot dihtrans.xvg and I should read the manual more carefully and analyze the outputs. 
Thank you again for your patience.

Behnoush

----- Original Message -----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Wednesday, January 30, 2008 2:43:49 AM (GMT+0330) Asia/Tehran
Subject: Re: [gmx-users] Dihedral restraints


If I understand what you're trying to do correctly, you want to measure the
dihedral of some given sequence of backbone atoms in your peptide and restrain
this angle to the starting value.  Is that much correct?  I've gotten lost a
bit in this thread as to your intent, and as Mark pointed out, it's getting
difficult to follow.  If that is indeed the case, then Xavier gave you the
answer already.  Use g_angle on your starting structure, using an index group
that specifies the appropriate atoms.  The manual has clear explanations on how
to do this measurement.  I performed a similar calculation on an arbitrary
structure I had around and it worked in less than 2 seconds.

-Justin

Quoting Behnoush Zare <bzare at iums.ac.ir>:

> Dear Mark,
>
> Ofcourse I'm worth your and others time since I reffered to some text and
> gromacs manuals as you and xavier suggest to me and I'm very appreciated. But
> I didn't give any clue. After all I try to be more precise about the replies.
>
> Behnoush
> ----- Original Message -----
> From: "Mark Abraham" <Mark.Abraham at anu.edu.au>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Wednesday, January 30, 2008 1:47:20 AM (GMT+0330) Asia/Tehran
> Subject: Re: [gmx-users] Dihedral restraints
>
> Behnoush Zare wrote:
> > Dear chris,
> >
> > According to your note about dihedral restraints, how I can calculate the
> torsional angles of the helix backbone. I performed it     using Deepview but
> it took long time. I think there should be more feasible one.
>
> Behnoush,
>
> So far your use of "measure" and "calculate" with regard to dihedral
> angles has been vague. I can't tell if you're trying to determine what
> these angles should be restrained to, determine what they are in your
> starting structure, or something else. Either way, the calculation is
> trivial.
>
> You should also have the courtesy to reply to the two people who've made
> suggestions for you, letting them know whether they've been successful
> in working out what you want. Otherwise, people may notice this and
> decide you're not worth their time :-)
>
> Mark
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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