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 >
