Hi yeo, I have one query related to the MD you are trying. What I understood here is you are trying different conformation of your protein molecule for docking it with ligand (please, correct me if I am wrong) I am also trying the same, But not finding any criteria to pick up the conformation of protein to try it further for docking ? Do you have any insight into the same ?
With Thanks, Vivek 2008/10/7 Justin A. Lemkul <[EMAIL PROTECTED]> > > > wk yeo wrote: > >> Hello, >> >> My responses are as follows: >> >> My questions: >>>> 1) Is it a good idea to use such catalytic domain structures for MD >>>> simulation? Or should I only use complete protein structures for MD? >>>> >>> That depends entirely upon what you are interested in simulating. >>> >> >> I am interested in predicting the binding energy (via further processing >> using a docking software) of a ligand to a specific protein target based on >> the conformation of the binding pocket after MD. How will missing residues >> in the other parts of the protein target affect the MD run for such >> purposes? >> >> > In biology, structure leads to function. Missing residues may lead to > spurious behavior, such as destabilization of the protein structure. > > 2) If I want to use Gromacs to conduct a MD of 0.1ps at 300K, do I need to >>>> constraint any atoms at the 'edges' during the MD run? >>>> >>> What kind of "edges?" Those that are adjacent to the missing segments? If >>> that's what you mean, see distance *restraints* or position *restraints*. >>> >> >> Yes, I meant atoms that are adjacent to the missing segments. When should >> I use distance restraints and when should I use position restraints? >> >> > Distance restraints are what you are probably looking for. You can fix the > distance between the backbone atoms to the distance found in the crystal > structure. As for whether or not you can be confident in doing so is up to > you. > > Position restraints are typically applied during solvent equilibration to > allow the solvent to orient around the solute. > > I have a new question: What if the protein-ligand complex structure >> obtained from PDB contains chloride ions? How should I handle any ions >> during the MD runs? Restraint them as well? Or should I just let them go >> through MD without any restraints? >> >> > If the ions were part of the precipitant or some sort of stabilizing > co-solvent, they may be unnatural and therefore safe to ignore. Adding (at > least) counterions to an MD simulation is routine, so you may end up adding > those ions back within during solvation. > > -Justin > > regards, >> wk yeo >> _________________________________________________________________ >> Manage multiple email accounts with Windows Live Mail effortlessly. >> http://www.get.live.com/wl/all >> >> > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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