RE: parameter request for PRES bonding

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Sun Oct 28 2018 - 18:09:06 CDT

That seems perfectly normal to me. You changed the atomtypes on C9 and NE2 (and some others it looks like, but I haven't been following your exploits all that closely), so any term that touches those atoms (and there are likely a ton of them) will be missing parameters. What behavior did you expect?

-Josh

On 2018-10-27 01:34:07-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

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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