(none)

Jennifer Ekstrom jennifer at BIO.CORNELL.EDU
Sat Mar 14 22:35:16 EST 1998


Hello again,

        I'm still having difficulties with my topology/parameter files.
I submitted coordinates to the XPLO2D server, and got a new parameter
file, and also added bond and angle lines to account for the C-N peptide
bond.  I am still getting errors in check, the latest being:

 %CODIMP-ERR: missing improper parameters %%%%%%%%%%%%%%%%%%%%%
  improper energy constant missing.
  target improper value missing.
  periodicity missing.
  ATOM1: SEGId="N   ",  RESId="79  ",  NAME="C   ",  CHEMical="CX3 "
  ATOM2: SEGId="N   ",  RESId="79  ",  NAME="CA  ",  CHEMical="CX2 "
  ATOM3: SEGId="N   ",  RESId="80  ",  NAME="N   ",  CHEMical="NH1 "
  ATOM4: SEGId="N   ",  RESId="79  ",  NAME="O   ",  CHEMical="OX4 "
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %CODIMP-ERR: program will be aborted.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 BOMLEV=    0 reached.  Program execution will be terminated.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 Subroutine DIE called . Terminating

        I've tried adding modifying improper info from param19x.pro or
parhcsdx.pro with no luck.  Xplor still crashes, this time printing 
an enormous list of close contacts.  If I delete the pvl group
from my pdb file, I'm able to run XPLOR with no problems.

Here is the current improper info in my pvl.top and pvl.par files:

from topology file:
 IMPRoper  CA   ON   C    CB  ! chirality or flatness improper    -4.57
 IMPRoper  C    CA   O    N   ! chirality or flatness improper    -4.47

from parameter file:
 IMPRoper CX2  OX1  CX3  CX5     750.0 0    0.000 ! Nobs =    1 ... Value =   -4.574
 IMPRoper CX3  CX2  OX4  NH1     750.0 0    0.000 ! Nobs =    1 ... Value =   -4.466


        Thanks in advance for any ideas,

Jennifer Ekstrom
Cornell Structural Biology
jennifer at bio.cornell.edu
(607)277-9440



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