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