AMBER Archive (2009)

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

From: Alan (alanwilter_at_gmail.com)
Date: Thu Aug 20 2009 - 03:28:09 CDT


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
>
>
>
>
>
>
>
>
>
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>

-- 
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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