[gmx-users] problem with ambconv

[Diane Fournier]

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
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