VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 16 2002 - 13:44:32 CDT

Dear Reinhard,
  Depending on how you aligned/docked these two separate structures
within VMD (i.e. using the "mouse move" feature, or via the atom
selection "move" and "moveby" commands..) you should be able to write
out the modified coordinates as two separate PDB files, then concatenate
them with a text editor or pdbcat, and then load that file and resave it
with VMD to fix up the atom index numbers etc. I just did this a minute
ago using the "mouse move" method to verify that having VMD perform all
of these steps and re-save the concatenated file does indeed recalcualte
the atom indices so you don't end up with multiple atoms with the
same index. :)

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Aug 16, 2002 at 04:41:54PM +0200, Reinhard Klement wrote:
> Greetings,
> I want to dock a drug molecule to a DNA structure with VMD. I can load
> both molecules into VMD and manipulate them in such a way that I can
> find the desired position for the drug. Now I want to run a simulation
> with this docked drug and DNA molecule. Is there a way to write a PDB
> file which contains both molecules in the rotated/translated position?
>
> Thank you in advance
>
> Reinhard Klement
>
> --
> Reinhard Klement
> Max-Planck-Institut für biophysikalische Chemie
> Abteilung Molekulare Biologie
> Am Fassberg 11
> D-37077 Göttingen
>
> GERMANY
>
> phone: +49 551 201 1389
> fax: +49 551 201 1467
>
> e-mail: rklemen_at_gwdg.de or reinhard.klement_at_mpi-bpc.mpg.de
>
> Web: http://www.mpibpc.gwdg.de/abteilungen/060 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078