[gmx-users] simulation with cofactor

Semen Esilevsky yesint4 at yahoo.com
Thu Jul 8 20:39:15 CEST 2004

> Hi every body
> I am facing some problem when i m doing the
> simulation of protein with 
> PLP cofactor. The initial pdb file has connect
> records for plp with protein= 
> But during the simulation PLP is coming out of the
> protein.
> Is this because the PLP-Protein connection is not
> defined in gromacs forcefeilds? 
> How can this be corrected?

In order to simulate the protein with some cofactor in
it you must have a topology for this thing. How did
you build the topology of your codactor? What
forcefield do you use? 

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