[gmx-users] file conversion from Amber to GROMACS for protein-ligand complexes

Andrew Voronkov drugdesign at yandex.ru
Fri Jun 26 17:03:34 CEST 2009

Dear GROMACs users,
we have a task to use Amber force fields for protein-ligand complexes for  GROMACS MD simulation.
Which strategy is better to use?
1. To make  .inpcrd and .prmtop files and then apply amb2gmx.pl script. Is output for the protein-ligand complex for this script will be correct?
2. Make .gro and .top files for ligand and protein separately and then to combine them to one .gro file and one .top file for protein-ligand complex simulation if it is possible.

Best regards,
Andrew Voronkov

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