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

Fenton Heirtzler fentonh at gmail.com
Fri Aug 28 13:13:56 PDT 2015

Hello Elaine,

Thank you for
time. The isophthalic acid hexamer is, in fact already known.
​I want to reproduce the hydrogen bonds in Chimera and which were reported
for its X-ray crystal structure, and not analyze a new X-ray structure.
Hence "detecting" hydrogen bonds is not the goal. Afterwards, I want to use
Chimera to predict the structure of a much more complicated compound which
also contains the isophthalic acid hexamer motif.

It was eventually possible to get Chimera to work for the simple isophthalic
acid hexamer. But the more complicated structure is making problems, and
that is why I am now writing you.

Here is what ended up working
​ for the "simple" isophthalic acid hexamer​
a. Assigning all atoms (as you pointed out, this may or may not have helped)
b. geometrically arrange  the 6 molecules' O-H bonds so that they point at
each other for H
c. Add H’s: yes;  Add charges: yes
​ (even though the structure already has all hydrogen atoms and has no

d. Use AM1-BCC
​, selecting the H-bonding option.​

However, I then tried the same procedure on the more complicated
derivative. The following message appeared "The bond number exceeds the
MAXBOND"....and Chimera then crashed. The more complicated molecule has 480
atoms & 522 bonds in total. 170 of the atoms are Hs attached to
: I tried "hiding" them, and it still crashed.

​The ​
"MAXBOND" descriptor is confusing: the AMBER manual refers once to it as
(maybe) a maximum bond length. But then the following link
​suggests that it is a number of bonds. And there is no mention of this
parameter in the Chimera user manual. ​
​I just want to press a button somewhere and enter in a new value so that
Chimera will not crash. Do you know if this is possible, or is my file just
too large for the program?​

​Thanks again


On Fri, Aug 28, 2015 at 10:52 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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”.
> <
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findhbond.html>
> 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
> <
> 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.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html>
> I hope this helps,
> 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 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
> >

Dr. Fenton Heirtzler
Phone: +1-301-312-5145
On LinkedIn
Skype: fentonheirtzler
Supporter of the International Day of Climate Action
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