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 <[EMAIL PROTECTED]> 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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