VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Nov 12 2018 - 01:50:29 CST

Hi:
I am trying to get bonding between protein HSP NE2 and an organic ligand
carbon, while imposing CGenFF atom types on both sides.

PRES ZAHI 1.449 ! patch for ligand to HSP bonding
> ! Patch must be 1-HSP and 2-ZPN
> ! use in patch statement
> ! follow with AUTOgenerate ANGles DIHEdrals command
> GROUP !
> ATOM 2C11 CG311 0.332 !
> ATOM 2C10 CG314 0.199 !
> ATOM 2H15 HGA1 0.09 !
> ATOM 2C9 CG2D2 0.127 !
> ATOM 2C8 CG2O5 0.333 ! CD2--NE2--CE1
> GROUP ! /
> ATOM 2CD2 CG2R51 0.219 ! C11--C10--C9--C8
> ATOM 2NE2 NG2R52 -0.133! |
> ATOM 2CE1 CG2DC1 0.349 ! H15
> DELETE ATOM 2H16
> DELETE ATOM 1HE2
> BOND 2C10 1NE2
> IMPR NE2 CD2 CE1 C10
> IMPR NE2 CE1 CD2 C10
>

However, the new atom names are only accepted for the ligand, not for the
protein, which conserved the original atom types CPH1 NR3 CPH2 for CD2 NE2
CE1, with bonding between C10 (CG314) and NE2 (NR3). pdb file shows zero
coordinated for CD2 NE2 CE1 on the ligand residue.

All that because I am trying to avoid parameterization for unusual bonds,
such as between CG314 and NR3, although I understand that with atom type
NG2R52 for NE2 a cascade of problems would arise on the protein side.

So, which is the best way to associate CGenFF to charmm36?

thanks
francesco pietra