AMBER: h bond analysis

From: Claire Zerafa <>
Date: Tue, 7 Mar 2006 06:39:52 +0100

Dear Dr Walker,

Sorry I am re sending this!! I think I sent it to your private address from
your website earlier. Sorry!!

i am loking at your tutorial regarding h bond analysis during a dynamics
I have some questions please

I am working on an androgen receptor, bound to different ligands
I am interested in writing out a script for ptraj.
obviously, it would be safe to follow your template with respect to the
donor acceptor nature of the standard amino acids
I know from the pdb file which the ligand protein contacts are-do i use
these to "personalise" my script?

List of putative hydrogen bonds between ligand R181000A and protein in PDB
entry 1E3G (back to top of page)

N - ligand atom number in PDB entry
Dist - distance () between the ligand and protein atoms
Surf - contact surface area (2) between the ligand and protein atoms
    Ligand atom Protein atom
----------------- ---------------------------- Dist Surf
  N Name Class Residue Name Class
 20 O83 II ARG 752A NH2 III 2.8 30.8
 20 O83 II GLN 711A NE2 III 3.9 0.2
 21 O97 I ASN 705A OD1 II 2.8 13.5
 21 O97 I THR 877A OG1 I 2.9 11.3
then again, in subsequent dynamics studies I change the ligand- so it is
quite possible that these hb interactions would change.

The trajectory files consider all of the protein. Is it possible to work
exclusively on active site amino acids only to decrease computer
I think I could most use some help in the personalisation of the script
though- I am working with pdb entry 1e3g.

Thank you very much


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Received on Sun Mar 12 2006 - 06:10:11 PST
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