[Chimera-users] Hydrogen bonding calculation issues with PDB2PQR/AMBER/CHIMERA

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 28 10:52:25 PDT 2015

Hi Fenton,
If you are just trying to detect the hydrogen bonds, I would definitely recommend using the FindHBond tool (in menu under Tools… Structure Analysis), or equivalently, the command “findhbond”.

If I understand correctly, PDB2PQR is not relevent to what you want to do.  PDB2PQR uses a web service to assign partial charges to atoms by lookup table.  Although its options include H-bonding stuff, that is only to allow it to add hydrogens if the structure doesn’t already have them. The different force field choices for PDB2PQR are different lookup tables, essentially, and the AMBER table only includes things like standard amino acids and nucleic acids, not your organic molecules.  When the web service does not find the atoms in the lookup table, you get zero atoms in the results.

Also, you do not need to change the names of the atoms.  As long as the names imply the proper elements, the atom types will be detected from the bond lengths and angles.

So theoretically, all you needed to do was read in your PDB file and use FindHBond.  If the structure didn’t have hydrogens, FindHBond would still work (it would “imagine” where the hydrogens could be), or you could use AddH (in menu under Tools… Structure Editing) before running FindHBond.  

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

On Aug 27, 2015, at 6:43 PM, Fenton Heirtzler <fentonh at gmail.com> wrote:

> Hello-
> I’m trying to use CHIMERA to model the hexameric hydrogen bonding of isophthalic acid. I’m just an organic chemist, not a computational chemist. The PDB2PQR subroutine is returning the reply “Error encountered: No heavy atoms found!”. Here is sequentially what I have done:
> 1.     A pdb file of isophthalic acid hexamer was imported.
> 2.     The covalent bond lengths and angles were set to realistic ones.
> 3.     The names of the concerned atoms were defined in the Build Structure/Modify Structure/Change Modified Residue’s name box, as described in the User Guide (i.e., Cac, O2, O3 and H)
> 4.     The default limits of 3.4 Å and 30° were used
> 5.     The AMBER force field was chosen.
> Thanks very much
> Fenton
> (PS – I’m a private person, not associated with either academia nor industry)

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