Re: AMBER: some bugfixes from Junmei Wang on 2004-05-04 (Amber Archive May 2004)

From: Junmei Wang <JWang.encysive.com>
Date: Tue, 4 May 2004 14:23:55 -0500

Hi, Oliver,
It is because the atom types are not correctly recognized by the atom type
program, which needs some clearly bond type information (aromatic single,
double etc). If flag "-5" in antechamber program is used, aromatic single
and double bonds are not discriminable. I have added several lines in
bondtype.C to solve this problem.. Please find the revised bondtype.C in
this email. Dave, would you please prepare another bugfix? Thank you very
much.

Best

Junmei

(See attached file: bondtype.C)

===============================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Email: jwang.tbc.com
Homepage: Http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================


             Oliver Hucke
             <ohucke.u.washing
             ton.edu> To
             Sent by: amber.scripps.edu
             owner-amber.scrip cc
             ps.edu Junmei Wang <JWang.encysive.com>
                                                                   Subject
                                       Re: AMBER: some bugfixes
             05/04/2004 01:12
             PM


             Please respond to
             amber.scripps.edu



Dear David Case and Junmei Wang,

thanks very much for the work on fixing the problem with mol2 files and
antechamber.

I just applied the bugfixes and checked the effect on the calculation of
bcc charges for pyridine.

It turns out that the results obtained with the pdb and the mol2 input
files are identical if the -j 5 option is not used. I used this option
because it is recommended in the amber8 manual (p. 85).
With the patch and -j 5 the atom types are assigned correctly but the
charges of the two carbons connected to the pyridine nitrogen and of
this nitrogen are still different from what is obtained without -j 5
(i.e. with -j 4) and either pdb or mol2 input.

In the attached file my input files and the output files obtained with
the different antechamber flags are given.

Best regards,
Oliver

David A. Case wrote:
> There are a couple of new bugfixes at the amber web site that should be
> noted:
>
> 1. If you try to use a "restraintmask" or "bellymask" string that has a
> distance constraint in sander, it will fail; (reported by Oliver
Hucke).
> Fixed with bugfix.7.
>
> 2. Problems with antechamber when mol2 files are used as input, and
particular
> problems with pyridine rings; (also reported by Oliver Hucke,
> http://amber.ch.ic.ac.uk/archive/200404/0305.html).
> Fixed with bugfix.6. [At least, we hope it is fixed; it will of
interest
> to see if this patch fixes the original poster's problem.]
>
> Also, for users of Amber 7: Junmei Wang has prepared some sample
"mopac.sh"
> files for the mopac508mn (and similar programs) and for mopac7 and
mopac8.
> Go to the Amber web site (http://amber.scripps.edu), the follow the links
> to "antechamber", then to "What's New".
>
> Thanks to Oliver Hucke for the error reports, and to Viktor Hornak and
Junmei
> Wang for the fixes.
>
> ...dave case
>

--
_______________________________________________________________
Oliver Hucke, Dr.
                               Health Sciences Building - K418C
University of Washington      1959 NE Pacific St.
Dept. of Biochemistry         phone: (206) 685 7046
Box 357742                    fax  : (206) 685 7002
Seattle, WA 98195-7742        email: ohucke.u.washington.edu
_______________________________________________________________
The output files with the commands used to get them:
antechamber -fi pdb -i pyr.pdb -fo ac -o testpdb.ac -nc 0 -c bcc
CHARGE      0.00 ( 0 )
Formula: H5 C5 N1
ATOM      1  C1  PYR     1       1.230   0.710   0.000 -0.246700        ca
ATOM      2  H1  PYR     1       2.162   1.249   0.000  0.142710        ha
ATOM      3  C2  PYR     1       0.000   1.420   0.000 -0.093230        ca
ATOM      4  H2  PYR     1       0.000   2.497   0.000  0.137400        ha
ATOM      5  C3  PYR     1      -1.230   0.710   0.000 -0.246680        ca
ATOM      6  H3  PYR     1      -2.162   1.249   0.000  0.142710        ha
ATOM      7  C4  PYR     1      -1.230  -0.710   0.000  0.392700        ca
ATOM      8  H4  PYR     1      -2.162  -1.249   0.000  0.021490        h4
ATOM      9  N   PYR     1      -0.000  -1.420   0.000 -0.664570        nb
ATOM     10  C5  PYR     1       1.230  -0.710   0.000  0.392690        ca
ATOM     11  H5  PYR     1       2.162  -1.249   0.000  0.021490        h4
BOND    1    1    2    1   C1   H1
BOND    2    1    3    7   C1   C2
BOND    3    1   10    8   C1   C5
BOND    4    3    4    1   C2   H2
BOND    5    3    5    8   C2   C3
BOND    6    5    6    1   C3   H3
BOND    7    5    7    7   C3   C4
BOND    8    7    8    1   C4   H4
BOND    9    7    9    8   C4   N
BOND   10    9   10    7   N    C5
BOND   11   10   11    1   C5   H5
----------
antechamber -fi mol2 -i test.mol2 -fo ac -o test.ac -j 5 -nc 0 -c bcc
CHARGE      0.00 ( 0 )
Formula: H5 C5 N1
ATOM      1  C1  PYR     1       1.230   0.710   0.000 -0.246700        ca
ATOM      2  H1  PYR     1       2.162   1.249   0.000  0.142710        ha
ATOM      3  C2  PYR     1       0.000   1.420   0.000 -0.093230        ca
ATOM      4  H2  PYR     1       0.000   2.497   0.000  0.137400        ha
ATOM      5  C3  PYR     1      -1.230   0.710   0.000 -0.246680        ca
ATOM      6  H3  PYR     1      -2.162   1.249   0.000  0.142710        ha
ATOM      7  C4  PYR     1      -1.230  -0.710   0.000  0.129700        ca
ATOM      8  H4  PYR     1      -2.162  -1.249   0.000  0.021490        h4
ATOM      9  N   PYR     1      -0.000  -1.420   0.000 -0.138570        nb
ATOM     10  C5  PYR     1       1.230  -0.710   0.000  0.129690        ca
ATOM     11  H5  PYR     1       2.162  -1.249   0.000  0.021490        h4
BOND    1    1    2    1   C1   H1
BOND    2    1    3   10   C1   C2
BOND    3    1   10   10   C1   C5
BOND    4    3    4    1   C2   H2
BOND    5    3    5   10   C2   C3
BOND    6    5    6    1   C3   H3
BOND    7    5    7   10   C3   C4
BOND    8    7    8    1   C4   H4
BOND    9    7    9   10   C4   N
BOND   10    9   10   10   N    C5
BOND   11   10   11    1   C5   H5
----------
antechamber -fi mol2 -i test.mol2 -fo ac -o test2.ac -nc 0 -c bcc
CHARGE      0.00 ( 0 )
Formula: H5 C5 N1
ATOM      1  C1  PYR     1       1.230   0.710   0.000 -0.246700        ca
ATOM      2  H1  PYR     1       2.162   1.249   0.000  0.142710        ha
ATOM      3  C2  PYR     1       0.000   1.420   0.000 -0.093230        ca
ATOM      4  H2  PYR     1       0.000   2.497   0.000  0.137400        ha
ATOM      5  C3  PYR     1      -1.230   0.710   0.000 -0.246680        ca
ATOM      6  H3  PYR     1      -2.162   1.249   0.000  0.142710        ha
ATOM      7  C4  PYR     1      -1.230  -0.710   0.000  0.392700        ca
ATOM      8  H4  PYR     1      -2.162  -1.249   0.000  0.021490        h4
ATOM      9  N   PYR     1      -0.000  -1.420   0.000 -0.664570        nb
ATOM     10  C5  PYR     1       1.230  -0.710   0.000  0.392690        ca
ATOM     11  H5  PYR     1       2.162  -1.249   0.000  0.021490        h4
BOND    1    1    2    1   C1   H1
BOND    2    1    3    7   C1   C2
BOND    3    1   10    8   C1   C5
BOND    4    3    4    1   C2   H2
BOND    5    3    5    8   C2   C3
BOND    6    5    6    1   C3   H3
BOND    7    5    7    7   C3   C4
BOND    8    7    8    1   C4   H4
BOND    9    7    9    8   C4   N
BOND   10    9   10    7   N    C5
BOND   11   10   11    1   C5   H5
The input files:
----------------
test.mol2 (obtained from pyr.pdb with antechamber)
.<TRIPOS>MOLECULE
PYR
   11    11     1     0     0
SMALL
No Charge or Current Charge
.<TRIPOS>ATOM
      1 C1          1.2300    0.7100    0.0000 ca        1 PYR       0.0000
      2 H1          2.1620    1.2490    0.0000 ha        1 PYR       0.0000
      3 C2          0.0000    1.4200    0.0000 ca        1 PYR       0.0000
      4 H2          0.0000    2.4970    0.0000 ha        1 PYR       0.0000
      5 C3         -1.2300    0.7100    0.0000 ca        1 PYR       0.0000
      6 H3         -2.1620    1.2490    0.0000 ha        1 PYR       0.0000
      7 C4         -1.2300   -0.7100    0.0000 ca        1 PYR       0.0000
      8 H4         -2.1620   -1.2490    0.0000 h4        1 PYR       0.0000
      9 N          -0.0000   -1.4200    0.0000 nb        1 PYR       0.0000
     10 C5          1.2300   -0.7100    0.0000 ca        1 PYR       0.0000
     11 H5          2.1620   -1.2490    0.0000 h4        1 PYR       0.0000
.<TRIPOS>BOND
     1    1    2 1
     2    1    3 ar
     3    1   10 ar
     4    3    4 1
     5    3    5 ar
     6    5    6 1
     7    5    7 ar
     8    7    8 1
     9    7    9 ar
    10    9   10 ar
    11   10   11 1
.<TRIPOS>SUBSTRUCTURE
     1 PYR         1 TEMP              0 ****  ****    0 ROOT
--------------
pyr.pdb
HETATM    1  C1  PYR     1       1.230   0.710   0.000        0.00
C
HETATM    2  H1  PYR     1       2.162   1.249   0.000        0.00
H
HETATM    3  C2  PYR     1       0.000   1.420   0.000        0.00
C
HETATM    4  H2  PYR     1       0.000   2.497   0.000        0.00
H
HETATM    5  C3  PYR     1      -1.230   0.710   0.000        0.00
C
HETATM    6  H3  PYR     1      -2.162   1.249   0.000        0.00
H
HETATM    7  C4  PYR     1      -1.230  -0.710   0.000        0.00
C
HETATM    8  H4  PYR     1      -2.162  -1.249   0.000        0.00
H
HETATM    9  N   PYR     1      -0.000  -1.420   0.000        0.00
N
HETATM   10  C5  PYR     1       1.230  -0.710   0.000        0.00
C
HETATM   11  H5  PYR     1       2.162  -1.249   0.000        0.00
H
CONECT    1    2    3   10
CONECT    2    1
CONECT    3    1    4    5
CONECT    4    3
CONECT    5    3    6    7
CONECT    6    5
CONECT    7    5    8    9
CONECT    8    7
CONECT    9    7   10
CONECT   10    1    9   11
CONECT   11   10
END

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application/octet-stream attachment: bondtype.C

Received on Tue May 04 2004 - 20:53:01 PDT