Hi, Do mind that calcium binding may involve (quantum) effects that are ill captured by classical force fields. If the binding site plays a central role in your research question, this may be problematic.
Cheers, Tsjerk On Oct 16, 2010 2:34 PM, "Justin A. Lemkul" <jalem...@vt.edu> wrote: leila karami wrote: > > Dear mohsen ramezanpour/ / > > yes. calcium is a typical ligand in my pdb ... There is no need to invoke PRODRG for any of this. Calcium ions are present in nearly all the force fields in Gromacs, and require no special intervention - pdb2gmx can handle them. PRODRG is only useful for small molecule topologies, (which are usually not so accurate) so passing it an entire protein is not going to work (as you can see). It will also fail with an error if you pass it a single Ca ion. -Justin -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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://lists.gromacs.org/mailman/listinfo/gmx-users ...
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