prob converting jmol to pdb

aishwarya · **Joined:** Mon Apr 20, 2009 10:19 am **Posts:** 3

can anybody help converting jmol to pdb. we want to dock calcium with a protien, but unfortuntely struck while loading ligand in pdb.
thanks in advance

bikadi · **Joined:** Wed Oct 29, 2008 2:24 pm **Posts:** 204

What is the ligand do you want to dock? DockingServer can dock small molecules to macromolecules, and not prepared to dock proteins to proteins right now.

aishwarya · **Joined:** Mon Apr 20, 2009 10:19 am **Posts:** 3

hello,
the ligand we wanted are calcium, magnesium and other metal ions. can use please guide us how to download these molecules in pdb format
thank you

bikadi · **Joined:** Wed Oct 29, 2008 2:24 pm **Posts:** 204

hello,

unfortunatelly, docking metal ions to proteins is not a traditional docking task and because of theoretical reasons this cannot be done correctly using any of the docking application. The reason for this is that this kind of calculation require quantum chemical methods and not force fields, while docking softwares are designed to find the best conformation of organic ligands interacting with proteins. The only working way I can recommend you, to carry out 1SCF calculation using the Mozyme functionality of MOPAC software, by changing the metal ions manually.

aishwarya · **Joined:** Mon Apr 20, 2009 10:19 am **Posts:** 3

thank you very much, i will try using with the other software. thank you once again