From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Nov 29 2006 - 12:31:59 CST

On Wed, 29 Nov 2006, Samuel C Flores wrote:

sam,

since this question has nothing to do with
the subject of the mail you are replying to,
please repost your mail, with a proper subject.

people that have to go through a lot of mail
use subject lines an mail-id (you can't see them,
but they are in the mails) to presort mails into
groups and look only at those where the topic
is interesting.

SF> Hi guys,
SF>
SF> I am trying to dock to a protein using autodock, and then run some dynamics
SF> using gromacs. I prepare the files using vmd. However VMD doesn't
SF> recognize the MN or MG atom types. Should I just replace these with ZN2?

what do you mean by not recongnize? VMD does not care at
all how you name your atoms...

please elaborate a little more.

axel.

SF> Does anyone know if this will be treated differently by GROMACS and
SF> AutoDock?
SF>
SF> Sam
SF>
SF> Samuel Flores
SF> Gerstein Lab
SF> office:
SF> 266 Whitney Ave., Bass 437
SF> New Haven, CT 06520
SF> 203.432.5405
SF>
SF> Home:
SF> 120 Huntington Street
SF> New Haven, CT 06511
SF> cell: 203.747.2682
SF>
SF> -----Original Message-----
SF> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
SF> Axel Kohlmeyer
SF> Sent: Tuesday, November 28, 2006 5:08 PM
SF> To: ivana adamovic
SF> Cc: vmd-l_at_ks.uiuc.edu
SF> Subject: Re: vmd-l: radius of the curvature
SF>
SF> On 11/28/06, ivana adamovic <iadamovic_at_gmail.com> wrote:
SF> > Dear all,
SF> >
SF> > Molecule of interest in my simulations is "curved" and its flexibility
SF> > comes from the change in curvature (radius) , or "end to end"
SF> > distance. Can I measure radius of the curvature using VMD?
SF>
SF> well, if you can define some set of 'backbone' atoms that define the
SF> curvature, you could write a script that monitors those coordinates
SF> and either -if they are in a straight line- just compute the sum of
SF> the distances, or -if they are more 'zig-zag'- use some kind of fitting
SF> to put a (spline?) function between those and compute the length
SF> of that.
SF>
SF> as a raw measure, you can for sure get the 'direct' end-to-end distance.
SF>
SF> cheers,
SF> axel.
SF> >
SF> > Thanks a lot for your help,
SF> >
SF> > Ivana
SF> >
SF> >
SF>
SF>
SF>

-- 
=======================================================================
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.