I am not sure what is the problem you have. Usually, I use O formated PDB files. It works well. I think you can report your bug to the Dr. A.M.J.J. Bonvin who is maintaining the server.
On Wed, Jun 9, 2010 at 6:08 PM, anil kumar <[email protected]> wrote: > Hello, > > I have tried HADDOCK recently and have got some parsing related error! > (indicative of some errors in the input PDB files.). I have checked my pdb > files and did not figure out anything wrong. > May I please get some suggestions about it from any of the experienced ones > in this area? > > regards, > Anil > > --- On *Wed, 9/6/10, Jiamu Du <[email protected]>* wrote: > > > From: Jiamu Du <[email protected]> > Subject: Re: [ccp4bb] Softwares for Protein-Protein docking! > To: [email protected] > Date: Wednesday, 9 June, 2010, 10:25 PM > > > Hi, > I suggest you to try HADDOCK if you have some interaction data, such as the > binding site, key residues, etc. It can use the interaction data as a > restrain and make the dock more accurate. And the web interface of the > HADDOCK server is very easy to handle. > Best wishes. > > On Tue, Jun 8, 2010 at 2:59 PM, xaravich ivan > <[email protected]<http://mc/[email protected]> > > wrote: > >> Dear CCP4 users, >> Though this is not directly linked to ccp4, i bet many of you have solved >> crystal structures of the ligand and receptor separately and tried to dock >> it. is there any program that docks two protein molecules. We have an >> overall idea where the protein will bind to the receptor. Is there something >> like AUTODOCK for macromolecules? >> >> It will be amzing if I get some suggestions. >> >> Thanks in advance, >> Ivan >> > > > > -- > Jiamu Du, Ph.D. > Postdoctoral Research Fellow > Laboratory of Structural Biology > Memorial Sloan-Kettering Cancer Center > RRL 269, 430 E 67th Street > New York, NY, 10021 > E-mail: [email protected] <http://mc/[email protected]> > Tel: (917) - 292 - 4616 > > > -- Jiamu Du, Ph.D. Postdoctoral Research Fellow Laboratory of Structural Biology Memorial Sloan-Kettering Cancer Center RRL 269, 430 E 67th Street New York, NY, 10021 E-mail: [email protected] Tel: (917) - 292 - 4616
