[gmx-users] GBSA with ligands

Leandro Bortot leandro.obt at gmail.com
Fri Oct 12 12:34:06 CEST 2012

Dear users,

     After parametrizing a ligand with antechamber and converting the
topology and structure files with acpype I can't do GBSA simulations in
GROMACS because of missing GB parameters. In fact, the implicit solvent
parameters weren't converted from the AMBER topology (.prmtop) to the
GROMACS topology (.top) by acpype.
     There is a "FLAG RADII" in the .prmtop but there is no [
implicit_genborn_params ] in the .top.

     Is this an issue with acpype?

     Any help would be greatly appreciated

Best regards,

More information about the gromacs.org_gmx-users mailing list