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

Fenton Heirtzler fentonh at gmail.com
Thu Aug 27 18:43:54 PDT 2015


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


(PS – I’m a private person, not associated with either academia nor

Dr. Fenton Heirtzler
Phone: +1-301-312-5145
On LinkedIn <http://www.linkedin.com/in/fentonhorgchem/>
Skype: fentonheirtzler
Supporter of the International Day of Climate Action <http://www.350.org/>
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