AMBER Archive (2009)

Subject: RE: [AMBER] antechamber am1-bcc issues

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Aug 20 2009 - 09:29:14 CDT

Hi Ilja,

I have not been following this thread in it's entirety but can I ask why you
are using mopac7? This code has a substantial number of bugs and I would be
very surprised if you get correct answers out of it. There are numerous
array overflows and missing initializations. Mopac 6 has similar bugs but
compiling it with g77 or gfortran with forced save and initialization of
variables can at least get it to be stable and give reasonable answers.
Compiling Mopac 7 with f2c (without any of these options) or in my
experience using other compilers such as ifort will NOT give you correct
answers and thus it should not be used.

We will shortly be replacing the use of Mopac in Antechamber with our own
code which will remove these issues.

For the time being you should ONLY use mopac 6 and ONLY compiled with g77 or
gfortran using the options specified in the Amber tools config and using the
DEFAULT Mopac control options specified by Antechamber. Nothing else has
been tested or has any warranty whatsoever.

Just my 3c...

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Khavrutskii, Ilja
> Sent: Thursday, August 20, 2009 4:38 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] antechamber am1-bcc issues
>
> Hi Alan,
>
> To run the mopac7-1.11 compiled with f2c stand alone, I simply modified
> the
>
> Amber/amber10/bin/mopac.sh wherever that is on your system to look like
> this:
>
> rm -f FOR0??
> ln mopac.in FOR005
> /usr/local/mopac7-1.11/src/mopac7 >& FOR006
> mv FOR006 mopac.out
> rm -f FOR0??
>
> Just copy the chunk I called input file into mopac.in
> and execute the .sh script by simply typing
>
> Amber/amber10/bin/mopac.sh in your prompt
>
> The energy I got (it is in mopac.out)
>
> FINAL HEAT OF FORMATION = -66.32321 KCAL
>
>
> TOTAL ENERGY = -1491.53165 EV
> ELECTRONIC ENERGY = -5828.77385 EV
> CORE-CORE REPULSION = 4337.24220 EV
>
> GRADIENT NORM = .00101
> IONIZATION POTENTIAL = 8.88503
> NO. OF FILLED LEVELS = 21
> MOLECULAR WEIGHT = 110.112
>
>
> SCF CALCULATIONS = 60
> COMPUTATION TIME = .763 SECONDS
>
> The final geometry I also provided in the first e-mail as a pdb.
>
> You should be able to get the same result by issuing the antechamber
> command that I provided.
>
> In some cases you might want to repeat the run by giving the
> antechamber mopac.pdb as an input, otherwise the geometry in the mol2
> file with be that of the intial (poor) guess.
>
> All the best,
> -Ilja
>
>
> On 8/20/09 4:28 AM, "Alan" <alanwilter_at_gmail.com> wrote:
>
> Hi Ilja,
>
> I am concern about it and I want to run some tests with mopac7-1.14 for
> Mac OSX.
>
> Would you please send me your inputs and outputs files (in private) so
> I can check things here. Testing with amber mopac I got the same
> problem your reported but for mopac7 I am not sure what to see because
> I didn't get any pdb output.
>
> If you could give more details about how did you test it with your own
> compiled version of mopac7 that I would appreciate.
>
> Many thanks in advance,
>
> Alan
>
> On Tue, Aug 18, 2009 at 22:00, Khavrutskii, Ilja<ikhavrutskii_at_ucsd.edu>
> wrote:
> > Comments regarding Antechamber.
> >
> >
> > 1. I did not notice any symmetrization of charges on atoms that are
> equivalent like (H-atoms of methyl groups, benzene molecule etc.)
> > 2. Geometry optimization is not working properly in standard
> Amber10 installation.
> >
> > I do not know if I am the only one experiencing these problems or
> not, and I will expand a bit more on problem 2 below:
> >
> > I was somewhat dissatisfied with the apparent inability of
> antechamber to get converged geometries for small molecules, like
> catechol for example. I am using the Amber10 standard installation on
> RH Linux box. Since antechamber is running mopac under the hood, and
> some time ago I used that program stand alone, I gave it a try to see
> if I can improve upon that PRECISE keyword. To my great surprise the
> mopac that is compiled with Amber (using Intel compilers) was not able
> to optimize a reasonable guess at all.
> >
> > The exact command I used was:
> >
> > antechamber -i catechol.pdb -fi pdb -o oh2bnz.mol2 -fo mol2 -c bcc -s
> 2 -at gaff -ek "AM1 ANALYT GRAD LET GNORM=1.D-8 SCFCRT=1.D-6 XYZ"
> >
> > This generates an mopac.in file that looks like this:
> >
> > AM1 ANALYT GRAD LET GNORM=1.D-8 SCFCRT=1.D-6 XYZ CHARGE=0
> > created by wmopcrt() for mopac
> >
> > C -0.0170 1 1.3780 1 0.0100 1
> > C 1.1690 1 2.0890 1 0.0020 1
> > C 2.3790 1 1.4200 1 -0.0130 1
> > C 2.4050 1 0.0350 1 -0.0210 1
> > O 3.5940 1 -0.6250 1 -0.0350 1
> > C 1.2110 1 -0.6800 1 -0.0130 1
> > O 1.2320 1 -2.0400 1 -0.0200 1
> > C 0.0020 1 -0.0040 1 0.0020 1
> > H -0.9600 1 1.9040 1 0.0260 1
> > H 1.1500 1 3.1690 1 0.0080 1
> > H 3.3040 1 1.9780 1 -0.0190 1
> > H 3.9460 1 -0.8200 1 0.8440 1
> > H 1.2460 1 -2.4380 1 0.8610 1
> > H -0.9260 1 -0.5570 1 0.0080 1
> >
> > The output looks like a big mess to me:
> >
> > SCF CRITERION = 0.1000E-05
> > CYCLE: 1 TIME: 0.06 TIME LEFT: 3599.9 GRAD.:999999.999 HEAT:-
> 54.21049
> > CYCLE: 2 TIME: 0.05 TIME LEFT: 3599.9 GRAD.:999999.999 HEAT:-
> 54.21157
> > CYCLE: 3 TIME: 0.02 TIME LEFT: 3599.8 GRAD.: 198.479 HEAT:-
> 21.66359
> > GRADIENTS OF OLD GEOMETRY, GNORM= 198.479378
> > -15.499537 57.227984 122.266395 1.431796 -3.530504
> 23.028728
> > -35.279682 -50.180782 -38.433267 -25.461497 -3.680921
> 6.443132
> > 15.413123 -45.601920 -37.698058 -13.430117 50.503021 -
> 4.669441
> > 34.211819 41.404541 11.990522 -34.282666 39.516530
> 3.591553
> > -30.807113 -11.363384 -6.427677 -2.833937 3.217770 -
> 3.782121
> > -21.071254 2.388208 -4.099834 9.610558 -17.402015 -
> 12.587598
> > GRADIENTS OF NEW GEOMETRY, GNORM=*************
> >
> ***********************************************************************
> *
> >
> ***********************************************************************
> *
> >
> ***********************************************************************
> *
> >
> ***********************************************************************
> *
> >
> ***********************************************************************
> *
> >
> ***********************************************************************
> *
> >
> >
> >
> > CALCULATION ABANDONED AT THIS POINT!
> >
> >
> > SMALL CHANGES IN INTERNAL COORDINATES ARE
> > CAUSING A LARGE CHANGE IN THE DISTANCE BETWEEN
> > CHEMICALLY-BOUND ATOMS. THE GEOMETRY OPTIMIZATION
> > PROCEDURE WOULD LIKELY PRODUCE INCORRECT RESULTS
> >
> >
> > It is clear that the installed version of mopac that comes with
> Amber10 is not compiled properly.
> >
> > If I follow the instructions for a stand alone mopac:
> >
> > http://sourceforge.net/projects/mopac7
> > And get f2c (which seems to be important) to compile it with:
> >
> > http://www.webmo.net/support/f2c_linux.html
> >
> > Then everything seems to get back to normal and I can optimize
> geometry to my satisfaction.
> >
> > In pdb format:
> >
> > ATOM 1 C1 CAT 1 -0.691 -1.620 0.126
> > ATOM 2 C2 CAT 1 0.704 -1.620 0.126
> > ATOM 3 C3 CAT 1 1.409 -0.418 0.126
> > ATOM 4 C4 CAT 1 0.706 0.790 0.124
> > ATOM 5 O5 CAT 1 1.318 2.026 0.119
> > ATOM 6 C6 CAT 1 -0.706 0.793 0.128
> > ATOM 7 O7 CAT 1 -1.447 1.951 0.128
> > ATOM 8 C8 CAT 1 -1.403 -0.422 0.127
> > ATOM 9 H9 CAT 1 -1.239 -2.573 0.126
> > ATOM 10 H10 CAT 1 1.252 -2.573 0.124
> > ATOM 11 H11 CAT 1 2.508 -0.414 0.125
> > ATOM 12 H12 CAT 1 2.273 1.885 0.137
> > ATOM 13 H13 CAT 1 -0.832 2.700 0.136
> > ATOM 14 H14 CAT 1 -2.502 -0.409 0.127
> >
> >
> > This kind of things get me really worried. Then David mentioned bond
> type issue...
> >
> > I would like to see any fixes to these problems if they are
> widespread.
> >
> > Thanks,
> >
> > -Ilja
> >
> >
> >
> >
> >
> >
> > On 8/7/09 2:19 PM, "David Mobley" <dmobley_at_gmail.com> wrote:
> >
> > All,
> >
> > I keep having issues with partial charges coming from Antechamber
> AM1-
> > BCC. In addition to the bug I mentioned previously relating to the -j
> > option resulting in incorrect charges when it should have no effect,
> > I'm also consistently finding that Antechamber generates
> substantially
> > different "AM1-BCC" partial charges than other implementations of
> AM1-
> > BCC. For a set of roughly 20 molecules, I obtained partial charges
> > from Christopher Bayly that he computed with his own, internal Merck
> > AM1-BCC implementation, and I also computed them with OpenEye's
> > Quacpac python toolkit. We then computed mean differences between
> > these charge sets. The Bayly AM1-BCC and OpenEye AM1-BCC
> > implementations agree extremely well, but Antechamber AM1-BCC charges
> > disagree with both Bayly and OpenEye partial charges reasonably
> > frequently.
> >
> > The differences are nontrivial -- they can make up to several
> kcal/mol
> > difference in computed hydration or binding free energies.
> >
> > I am attaching just one example of profound disagreement. The 2-
> > nitrothiophene.mol2 file contains Bayly AM1-BCC partial charges
> (sybyl
> > atom naming); 2-nitrothiophene_ante_amber.mol2 contains antechamber
> > AM1-BCC partial charges (amber atom naming), and 2-
> > nitrothiophene_oechem_amber.mol2 contains OpenEye AM1-BCC partial
> > charges.
> >
> > In this example, the Antechamber AM1-BCC charges differ from the
> > others by more than 0.3 e on the nitrogen alone.
> >
> > Anyway, I just wanted to put this out there to advise people. It
> > appears I will be ditching the Antechamber AM1-BCC implementation
> > until some of these problems are straightened out.
> >
> > Thanks.
> > David Mobley, Ph.D.
> > Assistant Professor of Chemistry
> > University of New Orleans
> > New Orleans, LA 70148
> > dlmobley_at_uno.edu
> > Phone 504-383-3662
> > Fax 504-280-6860
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28<<
>
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