[gmx-users] problem with ambconv

[David Mobley]

Diane,

I think we have used it with Amber 8 and Amber 9, probably also Amber
7, although in its current version it relies on being able to parse
prmtop files, which means that it is dependent on the amber8/9 prmtop
format. If this changed, it wouldn't work.

I'll send it along in just a moment.

Thanks,
David


On 8/4/06, Diane Fournier <diane.fournier at crchul.ulaval.ca> wrote:
> Thanks, yes, that would be interesting as I plan on obtaining AMBER.
>
> Does it work with any version ?
>
> Diane
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org on behalf of David Mobley
> Sent: Fri 8/4/2006 3:00 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] problem with ambconv
>
> Diane,
>
> We have an in-house script called amb2gmx written in collaboration
> with the Pande group that works for this purpose, although it requires
> an installation of AMBER. Let me know if you would like it.
>
> Thanks,
> David
>
>
> On 8/4/06, Diane Fournier <diane.fournier at crchul.ulaval.ca> wrote:
> >
> >
> >
> > Hi
> >
> >  I'm presently trying to use the ambconv program to convert amber topologies
> > generated with antechamber v. 1.26 and tleap to gromacs format for use with
> > the amber force field port.
> >
> >  The problem is, I can't get the program to work. For example :
> >
> >  $ ambconv -v -at spl2.atop -rst spl2.rst -gt spl2.itp -gro spl2.gro -pdb
> > spl2.pdb
> >  AMBCONV v1.0
> >  AMBER .top               : spl2.atop
> >  AMBER .rst               : spl2.rst
> >  GROMACS .top             : spl2.itp
> >  GROMACS .gro             : spl2.gro
> >  PDB .pdb                 : spl2.pdb
> >  Segmentation fault
> >
> >  This is using the old file format generated with tleap when setting
> > oldprmtopformat to on. The same happens with the new file formats (.prmtop
> > and .inpcrd).
> >  I have tried modifying the ambconv.c file and recompiling as suggested in
> > the mailing list (Wed Jun 16 18:41:55 CEST 2004), but got the same result.
> >
> >  Does someone has a version of ambconv which works with antechamber 1.26, or
> > should I use an older version of antechamber and leap ?
> >
> >  Diane
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read
> > http://www.gromacs.org/mailing_lists/users.php
> >
> >
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>