AMBER Archive (2004)

Subject: Re: AMBER: some bugfixes

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Tue May 04 2004 - 13:12:53 CDT

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_at_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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