e: [gmx-users] ambconv again

Alan alanwilter at gmail.com
Sun Mar 16 13:09:44 CET 2008

Hi Bruce, many thanks for your archive. Incidentally, I do use Mac!
and I have quitted trying to adjust Makefile for ambconv to compile on
Mac tiger intel.

Although your ambconv compiles here, it is still not working (giving
"Bus error").

But then you mentioned you did "topolbuild". So I fetched for it and
tried both in Mac tiger intel and Linux intel Ubuntu (with -lm).
In mac topolbuild fails with "Bus error" and in Linux it fails with
"segmentation fault". Antechamber 1.27 works fine here.

I hope I can solve this problems, but I must mention that your
topolbuild approach is a very good inspiration since I want to do
something similar from antechamber to generate CNS files with both
topologies PROSLQ and OPLS.

Many thanks,
> --- Alan <alanwilter at gmail.com> wrote:
> > Hi list!
> > I gave a good look at GMX mailing-list but I
> > definitely couldn't get ambconv
> > (from GMX website) working. I try the patch and I
> > still get "Segmentation
> > fault".
> >
> > I am using antechamber 1.27.
> >
> > Is there any kind soul with this ambconv package
> > fixed for Linux and working
> > with antechamber 1.27? I don't have amber and I am
> > not talking about the
> > perl version ambconv.pl.
> >
> > Could it be uploaded at GMX contribution session?
> > The ambconv there is from
> > 2002 and definitely doesn't work anymore.
> I've attached the version of ambconv I use.  It works
> on Mac OS X 10.3.9.
> I've not tried it on Linux, but it should work for
> you.
> After I got ambconv to work, I was not happy with the
> results with
> sybyl mol2 files.  Therefore, I wrote topolbuild to
> give me a gromacs
> topology directly.
> Sincerely,
> --
> Bruce D. Ray, Ph.D.
> Associate Scientist, and Operations Director
> NMR Center
> Physics Dept.
> 402 N. Blackford St.
> Indianapolis, IN  46202-3273

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.

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