Dear Thangavelu,
I have looked in my old files and I think you did not specify things
correctly. The way I did it was:
1) in the PRESidue definition: delete the lines with "1=Cys" and
"GROUP". Read this file in in the block where you read in the topology
files.
2) add the following patch statement e.g. before the disulfide loop:
patch DRGL reference=1=(resid 25) reference=2=(resid 501) end
If CNS did not change too much after I stopped using it, this shoudl
work.
Good luck!
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of Thangavelu K
Sent: Tuesday, October 19, 2010 12:45 PM
To: [email protected]
Subject: [ccp4bb] Reg. PATCH-ERR in CNS
Dear CCP4BB
We are having some problem in maintaining the covalent bond
between the Cys "Sulphur" and the inhibitor molecule during the CNS
refinement.
We have used the below given patch statement in the inhibitor
topology file and included the appropriate bond length angles and
dihedral angles in the inhibitor parameter file.
PRESidue DRGL
1=CYS (RESID 25), 2=DRG (RESID 501)
GROUP
DELETE ATOM 1H END
DELETE ATOM 2H END
ADD BOND 1SG 2C7
ADD ANGL 1CB 1SG 2C7
ADD ANGL 1SG 2C7 2CH
ADD ANGL 1SG 2C7 2C6
add DIHEdral 1CA 1CB 1SG 2C7
add DIHEdral 1CB 1SG 2C7 2C6
add DIHEdral 1CB 1SG 2C7 2CH
add DIHEdral 1SG 2C7 2C6 2O9
add DIHEdral 1SG 2C7 2C6 2C5
END {DRGL}
However we are getting the following error in the generate
output:
RTFRDR> set echo=false end
%RESIDUE-ERR: unrecognized command:
1=
^
%RESIDUE-ERR: unrecognized command:
1=C
^
%RESIDUE-ERR: unrecognized command:
1=CYS
^^^
^
%RESIDUE-ERR: unrecognized command:
1=CYS (RESID 25), 2=D
^
%RESIDUE-ERR: unrecognized command:
1=CYS (RESID 25), 2=DRG
and also the following error:
MAPIC: Atom numbers being modified
%PATCH-ERR: to be deleted bond -C +N not found in
molecular structure.
%PATCH-ERR: to be deleted angle -CA -C +N not found in
molecular structure.
%PATCH-ERR: to be deleted dihedral -CA -C +N +CA not
found in molecular structure.
%PATCH-ERR: to be deleted improper -C -CA +N -O not
found in molecular structure.
%PATCH-ERR: to be deleted improper +N +CA +CD -C not
found in molecular structure.
%PATCH-ERR: to be modified atom -C not found in molecular
structure.
%PATCH-ERR: to be deleted atom -O not found in molecular
structure.
MAPIC: Atom numbers being modified
%PATCH-ERR: to be deleted bond -C -OT1 not found in
molecular structure.
%PATCH-ERR: to be deleted angle -OT1 -C -OT2 not found in
molecular structure.
%PATCH-ERR: to be deleted dihedral -N -CA -C -OT2 not
found in molecular structure.
%PATCH-ERR: to be deleted improper -C -CA -OT2 -OT1 not
found in molecular structure.
SEGMNT: 222 residues were inserted into segment " "
However we continue the refinement and seen that the Cys "SH" is
moved a part (>2.8A) and the programs considers the Cys "SH" and the
inhibitor atom as non covalent atoms. Obviously the program is not
recognizing the patch commands. Could you please suggest us how to avoid
this problem.
Thanks,
Thangavelu
National University of Singapore.
