VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 29 2006 - 14:14:33 CST

Samuel,
  VMD is reasonably accepting of unusual atom names/types, but much depends
on whether you're loading structures from a file format that also provides
atomic element symbols, since many forcefields use different atom naming
schemes and VMD doesn't presently automatically deduce which forcefield
or program the atom names are intended for. If you have a PDB with the
atomic element symbol field populated, VMD will let you color by element
and will assign radii, mass, charges appropriately based on the element
information when available.
As for what names are acceptable in AutoDock and GROMACS, you
can probably find that out by looking at their documentation, unless
someone on VMD-L happens to know off the top of their head.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Nov 29, 2006 at 01:27:50PM -0500, Samuel C Flores wrote:
> 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.
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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