Help on PCA.

P.Rajesh Kumar rajesh at physics.iisc.ernet.in
Wed Mar 25 11:10:54 EST 1998


Hello,

	I am trying to refine a protein str with a non-standard aa
residue pyroglutamic acid, (PCA).  I have got the necessary files from
the Hic-up database from the Uppsala software factory.  When I use
those topology and param files in xplor-3.851, I get the following 
error messages out of checkstage.

-------------------------------------------------------------------
 POWELL>
 POWELL> end                                            {*Minimization is executed.*}
 POWELL: number of degrees of freedom=  4932
 %CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
  bond energy constant missing.
  target bond length missing.
  ATOM1: SEGId="PVXY",  RESId="1   ",  NAME="N   ",  CHEMical="NH3 "
  ATOM2: SEGId="PVXY",  RESId="1   ",  NAME="CA  ",  CHEMical="CX2 "
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
  bond energy constant missing.
  target bond length missing.
  ATOM1: SEGId="PVXY",  RESId="1   ",  NAME="N   ",  CHEMical="NH3 "
  ATOM2: SEGId="PVXY",  RESId="1   ",  NAME="CD  ",  CHEMical="CX7 "
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
  bond energy constant missing.
  target bond length missing.
  ATOM1: SEGId="PVXY",  RESId="1   ",  NAME="C   ",  CHEMical="CX3 "
  ATOM2: SEGId="PVXY",  RESId="2   ",  NAME="N   ",  CHEMical="NH1 "
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %CODBON-ERR: program will be aborted.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 BOMLEV=    0 reached.  Program execution will be terminated.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 Subroutine DIE called . Terminating

----------------------------------------------------------------------

	Any idea what I am doing wrong.  I would like to have suggestions
from you if you have faced any problems like this.  

Have a nice day.

rajesh




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