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

Justin A. Lemkul jalemkul at vt.edu
Sat Oct 16 14:33:08 CEST 2010

leila karami wrote:
> Dear mohsen ramezanpour/ /
> yes. calcium is a typical ligand in my pdb file.I used PRODRG server to make topology file but 
> ERRDRG> Too many atoms in this molecule (should be <=300).
> PRODRG> Program terminated unsuccessfully, sorry!

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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