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

Mon Aug 31 16:11:47 PDT 2015

Hi Elaine,

Thanks again for your time. Your explanation was very helpful.

Best

Fenton

On Mon, Aug 31, 2015 at 3:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Fenton,
> It sounds like you are trying to energy-minimize the structure.  Note this
> is not “predicting” the structure of a molecule, because it will just go to
> the local minimum energy well most accessible from the starting structure,
> which usually isn’t the global minimum.  Depending on the ruggedness of the
> energy surface, you could get a different result from each different
> starting conformation of the same molecule.
>
> However, putting that aside, let’s say you are trying to energy-minimize.
> You didn’t say that in your messages, but that’s my best guess since it
> will call other tools (AddH, AddCharge) to parametrize the structure
> beforehand.
>
> There is no need to say “yes” to adding hydrogens if your structure
> already has its hydrogens.  It’s not going to do anything in that case.
>
> Conversely, it is necessary to add atomic charges before
> energy-minimization.  Even if the molecule has no net charge, the
> individual atoms have partial charges.
>
> There is no H-bonding option to AM1-BCC charge calculation, it’s only an
> option for hydrogen addition (which was not done because the molecule
> already had hydrogens). MAXBOND is not something you can change in the user
> interface.  I believe it is a limit on the molecule size that is set in the
> AMBER code, and the message means that your molecule has too many bonds for
> this routine to handle.  You can choose the other charge calculation method
> (Gasteiger) instead of AM1-BCC.  It is simpler and more approximate but it
> may be your only choice for this molecule.
>
> After the charges are added, the minimization can run.
>
> I hope this clarifies things,
> 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 28, 2015, at 1:13 PM, Fenton Heirtzler <fentonh at gmail.com> wrote:
> >
> > Hello Elaine,
> >
> > Thank you for your 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-bonding.
> > c. Add H’s: yes;  Add charges: yes (even though the structure already
> has all hydrogen atoms and has no charge)
> > 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 carbon: 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/ContributedSoftware/findhbond/findhbond.html
> >
> > > <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
> results.
> > > <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
> >
> > >
> > > 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
> industry)
> > > >
> > >
> >
> >
> >
> > --
> > Dr. Fenton Heirtzler
> > Phone: +1-301-312-5145
> > On LinkedIn
> > Skype: fentonheirtzler
> > Supporter of the International Day of Climate Action
> > *********
> > _______________________________________________
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> > Chimera-users at cgl.ucsf.edu
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>
>

-- 
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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