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Hi Mareike, Did you also use Coot to fit the small molecule into the structure? If so, there might be some glitch at the stage of writing out the remodeled ligand... Do the coordinates for the small molecule look different within the input and output pdb files for the ligand when you look at the files manually? Yes, you do need to specify the top and param files in the input file so that the connectivity and atom parameters for your ligand are output correctly by generate.inp. Only other thing I can think of immediately is that the generate.inp file gives two choices for coordinate output format (either CNS format or O). Try writing out both ways and see if that helps. Couple of quick things to check. Raji ---------Included Message---------- >Date: 28-dec-2007 18:48:57 -0500 >From: "Mareike Kurz" <[log in to unmask]> >To: <[log in to unmask]> >Subject: [ccp4bb] problem with 'generate' (cns_solve) > >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 >[log in to unmask] > > > > > > > > ---------End of Included Message----------