Hi!
Thank you for this information. In fact, I was hoping that Modeller had some forcefields hidden somewhere in the depth of its code to do loop modelling around Ca2+ binding sites. The real problem is not to place the Ca2+, but to have all the oxygens of the different side chains point its way. My templates are not close enough to get this right, and I have even one case where the Ca-binding site is only present in the target.
In parallel, I try to get the sidechains in place using Amber, but modelling a Ca2+ binding site seems not to be a standard procedure (although this should occur quite often). Another problem with Amber is that I would have to keep the rest of my protein restrained (otherwise my structure would drift away from its crystall-structure status by completely resolving it in water - but I want to use the model for protein crystal structure building later). So the choice of these restrains turns out to be quite tricky as well.
So I am still wondering whether it would not be possible to teach MODELLER how to model a Ca2+ in its loop refinement algorithm. If someone could give me some technical advice on how to do this (or where to find more specific documentation) I would be very grateful.
Kind regards, Karsten.
On Tuesday 19 August 2003 21:04, Jim Procter wrote: > Hi. This is directed to : > >Karsten Suhre Karsten.Suhre@igs.cnrs-mrs.fr (IGS) > >Introduction of a Ca binding site > > > >Moshe Amitay moshe@noamy.ch.biu.ac.il ("Bar-Ilan University, Ramat-Gan, > >building a model with water molecules. > > From: Tjaart de Beer tjaart@tuks.co.za > > >Modelling with metals and hetero. > > The practical advice : > Modeller treats the 'hetatm' entries as residues for much of the modelling > process. By this, I mean that it is as picky as with the other residue > entries when you describe them in the alignment. You can see all the types > of residue entry that it knows about in the mod6v2/lib/restyp.lib file. > > Its always simpler to 'SET HETATM_IO', rather than change the pdb file. If > modeller knows about the heteroatom residue code then it will read it, and > not attempt to attach proximal metal ions to the polypeptide backbone. > > I was mislead by the chain break character '/', which actually introduces a > chain break for your model, rather than describing a corresponding template > (? not really sure here). I got away with this example : > 1tem:Template:1: :3: :.:.:. > WLMzz* > > 1hom:Homolog:1: :3: :.:.:. > WITzz* > > Where I just used set HETATOM_IO on. The important thing is the numbering > used in the PIR header for each protein sequence - this only relates to the > amino acids, not the hereroatoms. > > I imagine that you need to use set WATER_IO on, and put in the waters, too, > but the chain break didn't seem to help. > > Above all, look carefully at the numbers that Modeller gives you when it > complains that you don't have enough residues in the PDB file or the > sequence. For Moshe's case, the chain break may well have been the problem, > but it can't hurt to use the unedited PDB file but setting HETATM_IO as > well as WATER_IO (but maybe you could delete the un-necessary waters and > heteroatoms from the pdb file just to make the alignment simpler!). > > As for the optimization behaviour with metal atoms - I didn't really notice > modeller doing any optimization of the bonding geometry, but in my case > these contacts were thoroughly conserved. However, I can't see any > parameters in the MD forcefield definitions to indicate that charge/ligand > geometry is taken into account, it is probably all done through restraints. > > Think thats it - sorry for not giving a concrete example! > > j-- > > ps. For Calcium - the HETATM's residue entry should be CAL or CA (that is, > not CA2), and '3' is the alignment symbol used in the PIR file (see the > restyp.lib file). > _______________________________________________________________________ > Dr JB Procter:Biomolecular Modelling at ZBH - Center for Bioinformatics > Hamburg http://www.zbh.uni-hamburg.de/mitarbeiter/procter