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)