VMD-L Mailing List

From: Samuel C Flores (samuel.flores_at_yale.edu)
Date: Wed Nov 29 2006 - 12:27:50 CST

Resending -- just thought that last email needed a more descriptive subject
line ;)

Hi guys,

I am trying to dock to a protein using autodock, and then run some dynamics
using gromacs. I prepare the files using vmd. However VMD doesn't
recognize the MN or MG atom types. Should I just replace these with ZN2?
Does anyone know if this will be treated differently by GROMACS and
AutoDock?

Sam

Samuel Flores
Gerstein Lab
office:
266 Whitney Ave., Bass 437
New Haven, CT 06520
203.432.5405
 
Home:
120 Huntington Street
New Haven, CT 06511
cell: 203.747.2682

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Axel Kohlmeyer
Sent: Tuesday, November 28, 2006 5:08 PM
To: ivana adamovic
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: radius of the curvature

On 11/28/06, ivana adamovic <iadamovic_at_gmail.com> wrote:
> Dear all,
>
> Molecule of interest in my simulations is "curved" and its flexibility
> comes from the change in curvature (radius) , or "end to end"
> distance. Can I measure radius of the curvature using VMD?

well, if you can define some set of 'backbone' atoms that define the
curvature, you could write a script that monitors those coordinates
and either -if they are in a straight line- just compute the sum of
the distances, or -if they are more 'zig-zag'- use some kind of fitting
to put a (spline?) function between those and compute the length
of that.

as a raw measure, you can for sure get the 'direct' end-to-end distance.

cheers,
   axel.
>
> Thanks a lot for your help,
>
> Ivana
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.