Hi Rui, for some reasons, I also always encounter problems when building new ligand by CCP4 Sketcher. You can try PRODRUG ( http://davapc1.bioch.dundee.ac.uk/prodrg/index.html) to build your new ligand and get the cif from the server, it always works for me.
HTH, Matt 2009/11/27 rui <ruis...@gmail.com> > Hi, > > I found this old post in ccp4 and it's very useful. I used the same > procedure Scott described to add a ligand into pdb file. What I did, is in > coot, search for the ligand in the library and find the ligand and then > merge. However, when I tried to refine in refmac, it has some problems, it > complains about that "New ligand has been encountered, stop now". I didn't > create the cif file myself, it's been pulled from the library directory. Do > anyone know what could be wrong? Thanks a lot for your help. > > Thanks. > > On Thu, Feb 5, 2009 at 10:55 AM, Scott Pegan <pe...@uic.edu> wrote: > >> Andy, >> >> We do a lot of liganding fitting with CCP4. This is the general order of >> steps we take (post initial solution of the protein itself): >> >> 1) Build the potential ligand in CCP4 Sketcher >> >> a) Rename all the Hydrogens to H#, CCP4 Refmac has some issues with >> Hydrogens marked OH1, NH1, etc. To simplify things I normally just renumber >> all the Hydrogens starting from 1. Also makes for less hassle when using >> the definition file, as the labels in the definition file has to match the >> pdb of the ligand (this will be more important below). >> >> b) Use the regularize function with Refmac >> >> 2) Using Coot, load the protein and maps >> >> 3) Load the ligand and definition file (####_mon_lib.cif) >> >> 4) Use the find ligand function in Coot (find it under other modeling >> tools) >> >> a) select the protein, map you want to search >> >> 5) If you find results you desire, merge those ligands with the main pdb >> >> 6) Run Refmac on the merged PDB with the library for the ligand in the >> library input space. >> >> Hope this helps, >> >> Scott >> >> On Thu, Feb 5, 2009 at 9:27 AM, ANDY DODDS <andy.dod...@googlemail.com>wrote: >> >>> Hello, >>> >>> does anyone know of a tutorial which lays out some sort of pipeline, >>> hopefully using CCP4 packages, to fit and refine a small molecule >>> ligand please? >>> >>> cheers >>> >>> andy >>> >>> >> >> >> -- >> Scott D. Pegan, Ph.D. >> Senior Research Specialist >> Center for Pharmaceutical >> Biotechnology >> University of Illinois at Chicago >> > > -- -------------------------------------------------------------------------------------------- Matthew L.H. Chu, PhD The University of Manchester, UK Hong Kong Tel: (852) 26729515 [home] / (852) 9169 2427 [mobile] Email: linghonmatt...@gmail.com Facebook: http://www.facebook.com/MatthewLingHonChu MSN: chuling_...@hotmail.com Skype: matthew.lh.chu --------------------------------------------------------------------------------------------
