parameter request for PRES bonding

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Oct 27 2018 - 02:27:05 CDT

The following PRES generated correctly C9-NE2 bonding between organic
ligand and HSP of protein

> PRES ZAHI 1.116 ! patch for ligand-HSP bonding
> ! Patch must be 1-HSP and 2-ZPN
> ! use in patch statement
> ! follow with AUTOgenerate ANGles DIHEdrals command
> GROUP !
> ATOM 2C10 CG311 0.332 !
> ATOM 2C9 CG314 0.199 !
> ATOM 2H91 HGA1 0.09 !
> ATOM 2C8 CG321 0.127 ! CD2--NE2--CE1
>
 GROUP ! /
> ATOM 2CD2 CPH1 0.219 ! C10--C9--C8
> ATOM 2NE2 NR3 -0.20 ! |
> ATOM 2CE1 CPH2 0.349 ! H91
> DELETE ATOM 2H92
> DELETE ATOM 1HE2
> BOND 2C9 1NE2
> IMPR NE2 CD2 CE1 C9
> IMPR NE2 CE1 CD2 C9
>

Problems arise, however, on minimization. Besides the expected request for
BONDS
CG314 NR3 261.00 1.4900 !
CG311 HGA2 309.00 1.1110 !
ANGLES
HGA1 CG314 NR3 51.5 107.5 !
CG311 CG314 NR3 117.00 124.00 !
minimization also required angle
CG2O5 CG321 CG314
and many other angles outside the strict area of bonding. Even on
satisfying these requests, dihedrals were also requested.

Question: is that normal despite the <AUTOgenerate ANGles DIHEdrals> or did
I miss something?

thanks for advice
francesco pietra

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