VMD-L Mailing List

From: Umesh Ghoshdastider (fraternitydisposal_at_gmail.com)
Date: Wed Oct 21 2009 - 11:56:24 CDT

Hi there,

I recently started using vmd and having hard time solving following problems:

1. How can I align or superimpose two CG protein structures? I can't
do it in other software since it is CG and I had to write a script so
that vmd connects and colors the grains of the protein which other
softwares don't understand. Just manually moving molecules by mouse
does not work.

2. How can I count no. of other molecules (say resname abc) around the
given distance from the protein over time? Is it possible to color
those molecules, given the distance from the protein?

Thanks a lot for your trouble.

Best regards,
Umesh