GEN-RTP

Author

Jiaxing Zhang at Tianjin University (zhangjiaxing7137@tju.edu.cn)

Discriptions

An rtp and hdb file generator to be used together with the Sobtop program. It could handle the following problems:

Fix the wrong H names in the mol2 file, change all heavy atom names to "element+id" and overwrite the origin file
Generate the rtp file based on the itp file created by Sobtop program (follow the sobtop instructions)
Remove the atoms and corresponding bonds, angles, and dihedrals in the rtp file by the rules in the next section
Generate the hdb file based on the hydrogen rules
TODO: Leave the atomtype and ffnonbonded instructions to separate files for user to add the items manually

Bond, Angle, Dihedral, Improper Item Retain Rules

Bond: for AMBER force field, retain "-C"; for GROMOS force field, retain "+N"
Angle: Remove all exclude items
Dihedral: Remove all exclude items
Improper: Retain those only contain the connect atom