VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Oct 16 2018 - 10:13:08 CDT

Hi
I can't understand the error message in trying to bind the sp3 carbon C9 of
a ligand to the NE2 atom of HSP residue, which implies deleting the HE2
atom of HSP and the H91 atom at C9 of the ligand.

PRES ZAHI 0.661 ! patch for ligand to HSP bonding
> ! use in patch statement
> ! follow with AUTOgenerate ANGles DIHEdrals command
> GROUP !
> ATOM C10 CG311 0.303 !
> ATOM C9 CG314 0.17 !
> ATOM H91 HGA1 0.09 !
> ATOM C8 CG2D1 0.098 ! CD2--NE2--CE1
> GROUP ! /
> ATOM CD2 CPH1 0.19 ! C10--C9--C8
> ATOM NE2 NR3 -0.51 ! |
> ATOM CE1 CPH2 0.32 ! H91
> DELETE ATOM H91
> DELETE ATOM HE2
> BOND C9 NE2
> IMPR NR3 CPH1 CPH2 CG314
> IMPR NR3 CPH2 CPH1 CG314
>

the error message reads

       psfgen) no atom NR3 in residue HSP:227 of segment PROD

and therefore patching failed, while the .psf file shows that NE2 of HSP is
a NR3 type atom.

My PRES should be wrongly set. Thanks for advice.

francesco pietra