[Chimera-users] how to find salt bridge

[Elaine Meng]

Hi Bishwajit,
(A) The simple answer is to use FindHBond (or command findhbond) to find all H-bonds, and then just by eye identify which of those are salt bridges.

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>

See also this tutorial, there is an H-bonds section:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

(B) The long answer, if you really want to detect only the hydrogen bonds that are salt bridges, is to:
(1) Select formally charged H-bond donor and acceptor atoms,
(2) Use the FindHBond option to find only H-bonds with both ends selected. This option is in the GUI and is also available as a keyword of the findhbond command.

How to select charged donor/acceptor atoms:
The following command selects atom types in charged groups commonly found in amino acids and nucleotides, EXCEPT histidines:

select Ng+ | N3+ | N2+ | O2- | O3-

That's better than using residue names, because it also gets the free N-term and C-term and most charged ligand functional groups, and it is not necessary to specify "side chain only" to exclude neutral backbone hydrogen-bonding groups. However, we don't have a thiolate sulfur atom type; if there is specific Cys thiolate you wish to consider, you would have to add that sulfur to the selection manually.

Another caveat is that the selection command above does not include histidines. You could use the command:

select Ng+ | N3+ | N2+ | O2- | O3- | :his at nd1,ne2

but that would get nitrogens in neutral histidine sidechains as well as the positively charged. A more correct possibility with more steps is to: add hydrogens (AddH tool or command addh), add charge (Add Charge tool or command addcharge), and then use command:

select Ng+ | N3+ | N2+ | O2- | O3- | :/amberName=HIP & @nd1,ne2

(The charge assignment process identifies which histidines are doubly protonated and assigns them the AMBER residue name HIP.) There are additional atom types for charged functional groups, but they would not occur in proteins. If manmade ligands are involved, however, you may want to take a look at the list of atom types and possibly add N1+,P3+,S3+,S3- (no, that's not thiolate even though it sounds like it) to the selection command. 
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 4, 2012, at 7:58 AM, Bishwajit Das wrote:

> how to find salt bridge in a docked structure........plz help me