Re: [AMBER] problem with antechamber for C60

From: Dean Cuebas <deancuebas.missouristate.edu>
Date: Tue, 23 Mar 2010 15:13:37 -0500

Dear Chun-Wei,

Antechamber, like any computer program, needs to "guess" the correct "atom
types" . In your case, antechamber couldn't guess the correct hybridization
of your carbons.

So I read your coordinates into several different chemical structure apps,
and in fact, most could not correctly interpret and therefore draw the
correct buckyball structure, even with the CONECT records included with your
pdb. The point is that you want to get your structure assigned with correct
atom types before you put it into antechamber, and the Sybyl mol2 format is
the best for that.

(Chimera, Yasara Viewer, MacPymol, VegaZZ, Swiss-PDB Viewer, MarvinSketch
could not interpret the correct structure, VMD, Molegro Molecular Viewer and
Avogadro displayed the correct structure, but only Avogadro assigned the
correct atom types and bonds in the mol2 file that was saved. Of course,
this is not an exhaustive list of apps for this purpose. The point is that
a good general purpose organic structure app is needed to recognize atom
types and bonds in tricky situations.)

The file fullerene.mol2 that I have included shows the Sybyl mol2 atom types
and bonding type (at the bottom) correctly assigned and file fullerene2.mol2
is the output of antechamber showing the correct atom type (ca).

Also note the charges in the last column... here again, human intuition is
needed. In C60, all the carbon atoms are chemically and electronically
identical, so there should be zero partial charge associated with these.

Using

parmchk -i fullerene2.mol2 -f mol2 -a Y -o fullerene2.frc

gives the forcefield parameters (in file fullerene.frc)

You need to check these... the improper torsion is set to 180 degrees and
that is fine for planar aromatics, but not fullerenes.

In fact, you may not even need an improper term here
(ok people, help me out here...)

I hope this helps as you continue to learn, like I am.

Dean

Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897



> From: Chun-Wei Pao <barbarossapao.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Tue, 23 Mar 2010 01:10:59 -0500
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] problem with antechamber for C60
>
> Dear Amber users
>
> I am trying to use antechamber to generate GAFF parameters for simulation of
> C60 clusters. However, I found the following error:
>
> I key in
>
> $AMBERHOME/bin/antechamber -i fullerene2.pdb -fi pdb -o fullerene.mol2 -fo
> mol2 -c bcc
>
> and get
>
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase PSCUTOFF in define.h and recompile bondtype.c
> Be cautious, use a large value of PSCUTOFF (>100) will significantly
> increase the computation time
>
> Error: cannot run "/home/cwpao/amber11/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit
>
>
> Enclosed is the PDB file of the C60. Could anyone tell me what happened? I
> suspect that this is due to the pentagon C atoms.
>
> Thanks!
>
> C.W.



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Received on Tue Mar 23 2010 - 13:30:04 PDT
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