[gmx-users] How to use ambconv

[Maik Goette]

When I remember correctly, ambconv is slightly buggy.
I have a working version here, but in the case of Amber8 you have to 
modify the amber output file a bit, to get it working.
After that, it works quite nice.
Nevertheless, I would suggest using the sorin port of the amber FF. It 
works also quite nice so far and yields similar results like the ambconv 
topologies.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Bob Johnson wrote:
> Hello everyone,
> Is there anything special you have to do when using ambconv? I downloaded this
> program today from the Gromacs website and am having problems with it. I'm
> trying to convert topology and coordinates generated using Amber7. I give the
> following command:
> 
> ambconv -at amber.atop -gt gromacs.top -rst amber.rst -gro gromacs.gro -pdb
> gromacs.pdb
> 
> I get the following message:
> AMBER .top               : amber.atop
> GROMACS .top             : gromacs.top
> AMBER .rst               : amber.rst
> GROMACS .gro             : gromacs.gro
> PDB .pdb                 : gromacs.pdb
> Segmentation fault
> 
> Does anyone know how to use this?
> Thanks,
> Bob Johnson
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