[gmx-users] ligand parameterization for amber port in gmx

merc mertens merc.mertens at gmx.net
Wed Sep 17 17:46:19 CEST 2008

Dear people,

I have parameterized a ligand with one phosphate and one pyrophospate group
using antechamber with AM1-BCC charges and the GAFF forcefield. Amber files
were converted to gmx files (*.itp/*.top and *.gro) with the amb2gmx
conversion tool (http://www.alchemistry.org/wiki/index.php/Free_Energy_Tools)
and then used in gromacs for energy minimization. The geometry looks fine
after in vacuo EM and EM in water (ffamber tip3p model from amber ports) of
the ligand alone (not bound to protein!). Minimizing the ligand in its
binding mode as seen in the corresponding PDB (using the amber03 ff) also
works fine if magnesium ions are NOT included. Including magnesium ions
however leads to severe deformations of the phosphate and pyrophosphate
groups. I suspect it has something to do with not including the magnesium
ions in the parameterization. Can anybody please give me a hint on how to
solve this problem?

Thanks a lot,
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