VMD-L Mailing List

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Mon Aug 22 2005 - 14:11:22 CDT

I'm not very familiar with VMD. I'm not trying to overlay structures
to compare them. I need to overlay two drug molecules (they have
different structures) so that the new one is in the same space in the
DNA as the old drug. This is based on matching three or four atoms
only, not the entire structure. (I can only get the align function to
work in VMD when the molecules have exactly the same atoms.) I then
need to save the new drug's new coordinates so that I can then use the
new, merged, pdb as an input file for AMBER.

Any help would be greatly appreciated. Please keep explanations simple
(real examples are good) as I'm not an experienced user. I've been
mainly using VMD as described in the AMBER tutorials to visualize
trajectories and have learned how to do representations, but that's
about it. I'm used to using the graphical interface, not the line
command.

Thank you very much,

Kara Di Giorgio

On Aug 22, 2005, at 9:11 AM, John Stone wrote:

>
> Hi,
> You can do RMS alignments in VMD with one of several methods.
> The VMD molecular graphics tutorial includes basic instructions for
> doing this with text commands (see "aligning two molecules"):
>
> http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node3.html
>
> You can also do this with the Analysis->Multiple Alignment
> or Analysis->RMSD Calculator extensions included in VMD 1.8.3,
> or with the RMSDTT extension here:
>
> http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/
> rmsdtt/
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Aug 19, 2005 at 02:26:32PM -0700, Kara Di Giorgio wrote:
>> I'm trying to overlay two drug molecules in a binding site of a DNA
>> strand from a pdb file. I've read in the manual that you can overlay
>> structures in VMD, but I've never been able to understand how to get
>> it
>> to work. I've been getting help with this from a friend who knows
>> MIDAS. In MIDAS it's relatively easy, you give it the match command
>> and then pick the four atoms of each structure you want to match.
>> However, the computer that has MIDAS is not convenient to access ( a
>> VERY old SGI) and I'd like to be able to do something similar on my
>> Mac. Has anyone done this before and would someone be willing to talk
>> me through it?
>>
>> Thank you in advance,
>>
>> Kara Di Giorgio
>> University of the Pacific
>
> --
> 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
>