AMBER Archive (2004)
Subject: Re: AMBER: some bugfixes

From: Junmei Wang (JWang_at_encysive.com)
Date: Tue May 04 2004 - 14:23:55 CDT

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In reply to: Oliver Hucke: "Re: AMBER: some bugfixes"
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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_at_tbc.com
Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================

             Oliver Hucke
             <ohucke_at_u.washing
             ton.edu> To
             Sent by: amber_at_scripps.edu
             owner-amber_at_scrip cc
             ps.edu Junmei Wang <JWang_at_encysive.com>
                                                                   Subject
                                       Re: AMBER: some bugfixes
             05/04/2004 01:12
             PM


             Please respond to
             amber_at_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_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

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

application/octet-stream attachment: bondtype.C

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Next message: FyD: "Re: AMBER: reproduction of RESP charges for Gly"
Previous message: David A. Case: "Re: AMBER: Normal Mode Analysis possibility"
In reply to: Oliver Hucke: "Re: AMBER: some bugfixes"
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AMBER Archive (2004)Subject: Re: AMBER: some bugfixes

AMBER Archive (2004)
Subject: Re: AMBER: some bugfixes