[gmx-users] RV: pregunta per la gromacs list

Jordi Camps jcamps at lsi.upc.edu
Mon May 30 18:03:29 CEST 2005

On behalf of one of my work mates:

Hi I'm trying to convert a restart file from amber to gromacs. I'm using
truncated octahedric box of water and I'm not able to convert the
orientation of the box from amber to gromacs. I know that amber applies a
rotation after the box construction (amber constructs octahedric boxes using
a cubic box and cutting off the corners), this rotation is done in order to
orientate that box for pme calculations, this rotation is 45º around Z axis
90 º around X axis and 35.264 around Y axis. 
I've tried to apply reverse these rotations with editconf but it does'nt
work. I've applied other transformations (like the transformation suggested
in editconf help for gromos structures but any succesful result is obtained.

When I'm trying to visualize my original molecule or rotated ones in the -ur
rect option in trjconv very weird results are obtained.
Any hint or suggestion, thanks a lot in advance

Carles Ferrer-Costa				tel +34934037155
Molecular Modelling and Bioinformatics		fax +34934037157
IRBB-Parc Cientific de Barcelona. UB		e-mail:gandalf at mmb.pcb.ub.es

Josep Samitier, 1-5 08028 Barcelona.

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