Hi Dear users, I have started to do calculations of the binding between a protein and different ligands. I have read articles on the LIE method and one tutorial. But still I have some quite general questions. I am using Cut-off and NVT ensamble.
1. When I run my ligands in a water solution without the protein, should I add counterions (Cl and Na) at physiological concentrations (about 10mM to 100mM) or make the system neutral with one or two ions or can I ignore any ions the simulation. 2. Should I put any restraints on the ligand in the simulation without the protein? 3. When I run my ligand bound to the protein. Should I put restraints (c-alpha, all atoms) on both protein and ligand or only protein or ligand or neither of them? My initial thought would be to put restraint on c-alpha of the protein and let the rest of the system be "free". Mikko ____________________________________________________ One cannot avoid making mistakes if one tries to produce a set of words, or of mathematical formulae, to describe nature. Nature is more complicated than language or mathematics. Nevertheless, one must do one's best to produce a set of symbols which are not to discordant with the facts. J.B.S. Haldane, preface to "What is Life?", Lindsay Drummond, 1949
begin:vcard n:Hellgren;Mikko fn:Mikko Hellgren tel;cell:+46-737280550 tel;fax:+46-8-338453 tel;work:+46-8-52487747 org:Karolinska Institutet;Department of Medical Biochemistry and Biophysics adr:;;Scheeles väg 2 Scheelelaboratoriet;Stockholm;;SE-171 77 ;Sweden version:2.1 email;internet:[EMAIL PROTECTED] title:Graduate Student end:vcard
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