[gmx-users] Fwd: Using amber-ff14SB forcefield port to GROMACS - blowing up error

[p.kartheek]

Dear experts,
Currently I am trying to model Protein-DNA complex systems, with updated
Amber forcefield parameters. Parmbsc1 for DNA and *ff14SB* for protein,
considering the unavailability of theses updated forcefield ports within
gromacs, I have managed to generate the topologies through tleap module of
ambertools. Latter these topologies were translated to gromacs format using
"ParmED". However, I am not able to proceed beyond minimization step due to
hydrogen atoms related blowing up error. I want to do equilibration by
applying restraints on only heavy atoms of the systems excluding hydrogens.
But don't know how to generate posre files for only heavy atoms as the
make_ndx doesn't showing any option to exclude hydrogens in water and DNA.
I can use grep to get all the indices of hydrogens from the gro file but is
there anyway to supply file where the information of heavy atoms is saved
instead of entering values manually. Any kind of the help will be highly
appreciated.
Thanks in advance.

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P. Kartheek,
PhD Candidate, Computational Biophysical Chemistry,
Center for Computational Natural Sciences and Bioinformatics,
International Institute of Information Technology,
Marimuthu Krishan Group,
9701577399,
kartheek.p at research.iiit.ac.in,