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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