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.
