[gmx-users] simulation of a protein including calcium ion

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Oct 16 18:49:34 CEST 2010


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.



On Oct 16, 2010 2:34 PM, "Justin A. Lemkul" <jalemkul at 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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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