[gmx-users] TOPOLBUILD 1.3

Ray, Bruce D bray at iupui.edu
Mon Feb 27 16:16:15 CET 2017

> Date: Mon, 27 Feb 2017 07:26:23 +0000
> From: "Subashini .K" <subashinik at hotmail.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] TOPOLBUILD 1.3
> Message-ID:
> 	<SG2PR06MB1712153D90F961B3FF525873D4570 at SG2PR06MB1712.apcprd06.prod.outlook.com>
> Content-Type: text/plain; charset="iso-8859-1"
> Hi gromacs users,
> I want to use oplsaa force field for my organic compound.
> Can anyone tell me how to install topolbuild 1.3 and thereby generate .GRO, .ITP and .TOP with opls-aa parameter incorporated in it?
> Thanks,
> Subashini.K

Note that the source directory is in the directory "src'.

1. In the topolbuild source directory, change the defines in judge_types.h to read:
#define MAXLEVELS 16
#define MAXCHAIN 16
#define MAXENVBOND 16
#define MAXENVSTR 48
#define MAXSCAN 80
#define NULLCHAR 0
#define NUM_FEAT 25

2. In the source directory, follow the instructions in INSTALLATION.txt which reads:

Compilation has been tested on a G4 Power Macintosh running Os X 10.3.9
with both gcc version 3.3  20030304 (Apple Computer, Inc. build 1671), 
and with gcc version 4.1.0 as distributed by the Fink Project.

Two make files, that may need editing for individual systems, are included
as follows:
     Makefile                        Uses a standard C compiler with option -O
                                     to build the executable topolbuild
     Makefile.G4OsX                  Optimization set for a G4 Power Macintosh
                                     running Os X with optimization options
                                     -O2 -mcpu=7450 -mtune=970
To build topolbuild, type
If you happen to have a Mac PowerPC G4 running Mac OS X, you can also type
     make -f Makefile.G4OsX
Otherwise, your system may require editing of the make file according to
the specifications of your systems C compiler and libraries to generate a
functional program.  Advice on such editing is best gotten from your own
technical support people.

3.  To use, follow the instructions given in README.txt
    The *.top generated will need to be correct for gromacs 3.3 and can be
    converted for more recent gromacs versions with your favorite *NIX text editor.

Bruce D. Ray, Ph.D.
Associate Scientist
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202

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