Dear All,

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

Another qestion, I can I use the optimize command? Thanks for your help,

Ricardo Leite

On Mon, Mar 01, 2004 at 07:10:57AM -0800, Shamshad Zarina wrote: > I am interested in adding ligand like glucose to one > particular residue in my protein (which is not present > in my template). Any ideas?

If the ligand's not present in the template, then Modeller has no way of predicting its structure. So, you have three options:

1. Add another template which has the ligand in it, and see http://salilab.org/modeller/FAQ.html#4 Use the BLK residue type in your alignment, and Modeller will copy the ligand directly from the template.

2. Define topology and parameters for the ligand: see http://salilab.org/modeller/FAQ.html#17 Use the new residue type in your alignment, and Modeller will attempt to model the ligand using a molecular mechanics force field.

3. Add the ligand to the model after generation by hand, or using a modeling package.

Ben Webb, Modeller Caretaker