[gmx-users] hydrogen atom parameter definition for charmm 36

Nikhil Maroli scinikhil at gmail.com
Sat Apr 9 14:42:41 CEST 2016

Dear all,

i m doing mmpbsa calculation using GMXPBSA tool ,for protein ligand complex
during the steps i invoked the command
  pdb2gmx -f _comp0.pdb -p topol_comp.top -i posre_comp.itp -o _comp0.gro
-ignh -water tip3p

i have generated the ligand topology such as *.itp and *.prm file ,but it
looks like i cant  insert those in topology as doing usually ,in order to
edit topology database,can anyone give me the details of *.hdb file
VAL     5
1   1   HN  N   -C  CA
1   5   HA  CA  N   C   CB
1   5   HB  CB  CA  CG1 CG2
3   4   HG1 CG1 CB  CA
3   4   HG2 CG2 CB  CA

what is HN N -C CA?

is there any automatic tool for this available?

forcefield charmm36

Nikhil Maroli

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