I am refining a structure in which I had to model a small molecule
(done with Dundee PRODRG2 server). After fitting the small molecule
into the structure I merged the pdb's and used the merged pdb file
for "generate" (cns_solve). (Just in case: I did put the top and par
file for the small molecule into the input file).
In the obtained pdb.file from generate-the coordinates for the small
molecule have changed in a way, that by loading this pdb into Coot,
the molecule is not drawn properly anymore and appears at a random
place in the structure.
In the output file from 'generate', I get the following error message:
COOR>REMARK
COOR>HETATM 1 OAA DRG 1 6.470 4.170 1.460 1.00
20.00 O
%SEGMNT-ERR: attempt to enter duplicate residue 1 DRG
%SEGMNT-ERR: attempt to enter duplicate residue 1 DRG
%SEGMNT-ERR: attempt to enter duplicate residue 1 DRG
%SEGMNT-ERR: attempt to enter duplicate residue 1 DRG
%SEGMNT-ERR: attempt to enter duplicate residue 1 DRG
%SEGMNT-ERR: attempt to enter duplicate residue 1 DRG
COOR>CONECT 2 1 3
COOR>CONECT 3 2 4 5
COOR>CONECT 4 3
COOR>CONECT 5 3 6
COOR>CONECT 6 5
COOR>END
CHAIN> end
SEGMENT> end
and then later on:
COOR>REMARK
COOR>REMARK
COOR>HETATM 1 OAA DRG 1 6.470 4.170 1.460 1.00
20.00 O
COOR>HETATM 2 CAD DRG 1 6.320 4.540 0.090 1.00
20.00 C
COOR>CONECT 2 1 3
COOR>CONECT 3 2 4 5
COOR>CONECT 4 3
COOR>CONECT 5 3 6
COOR>CONECT 6 5
COOR>END
%READC-WRN: multiple coordinates for 6 atoms
%READC-WRN: still 886 missing coordinates (in selected subset)
CNSsolve> set echo=off end
I am fairly new to solve a structure including another small molecule
and would really appreciate if someone could give me some advice.
Thank you very much in advance,
Mareike
Mareike Kurz
[EMAIL PROTECTED]
