VMD-L Mailing List

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Wed Aug 12 2009 - 14:48:23 CDT

I have constructed a pdb model of a compound and am trying to place it in my protein. When I do this I open up both protein pdb and my compound pdb simultaneous in VMD. The problem is when I try to position the compound into the pocket of the protein. I cannot seem to move it closer in the sense that no matter how long I freeze the protein and move the compound it never appears to get closer. Is this just because it is VERY difficult or is there some barrier to doing this. I attempted it for quite some time and could never get the compound positioned correctly. Is there a way to do this with VMD. I am using the WINDOW version.

Thanks, Steve