On Tue, Mar 02, 2004 at 02:06:19PM +0000, rleite@ualg.pt wrote: > I need some help to insert some Cl atom and attach to my atom file. The atoms > are: > HET CL A1174 1 > HET CL A1175 1 > HETNAM CL CHLORIDE ION > FORMUL 2 CL 2(CL1 1-) > FORMUL 3 HOH *119(H2 O1) > > HETATM 887 CL CL A1174 -48.597 14.617 -86.523 1.00 42.42 > CL > HETATM 888 CL CL A1175 -43.313 22.617 -80.666 1.00 46.05 > CL > HETATM 889 O HOH Z 1 -22.832 8.494 -87.572 1.00 41.36 > O > HETATM 890 O HOH Z 2 -24.042 4.420 -89.079 1.00 58.80 > O > HETATM 891 O HOH Z 3 -24.444 9.116 -90.286 1.00 32.67 > O > HETATM 892 O HOH Z 4 -23.398 7.438 -99.414 1.00 45.67 > O > HETATM 893 O HOH Z 5 -25.681 7.217 -92.041 1.00 44.81 > O > HETATM 894 O HOH Z 6 -21.582 10.893 -97.569 1.00 30.12 > O
Looks like a simple case of cut-and-pasting the atom information into one of your template PDB files. What problem are you having?
See also http://salilab.org/archives/modeller_usage/2004/msg00094.html
> Another qestion, I can I use the optimize command?
There is documentation and an example at http://salilab.org/modeller/manual/node115.html
Ben Webb, Modeller Caretaker