VMD-L Mailing List

From: BERGY (nucleic81_at_gmail.com)
Date: Thu Apr 24 2008 - 05:42:53 CDT

dear friends,
 i have 89 protein pdbs bound to DNA. Of which some have more then 3
protein interacting with DNA and the rest not having contact. i want
to study the protein DNA interface , so i wish to make files that will
seperate for each interface. so how to identify the chains that are
contacting the DNA. Will 5 Angstrom sphereical cut off around each
Phosphate atom will do it ?? Or should i scan for all possible H2
bonds and see wat chains are involved? is there a optinon in VMD for
this to assign the HB cut off for to 5Angstrom and run it for whole
pdb file.. suggest any other program availabel to study the DNA
-Protein interface like say NUCPLOT .