[gmx-users] use of PRODRG

Justin Lemkul jalemkul at vt.edu
Wed Sep 19 11:23:28 CEST 2012

On 9/18/12 10:35 PM, Elie M wrote:
> Dear all,
> I have been reading about PRODRG that takes a PDB file as an input and produces topologies compatible with GROMACS as an output. Can this program be then considered as a solution to the problem of missing residues in GROMACS like LIG?

PRODRG produces topologies for the Gromos96 43a1 parameter set (and an older 
version produces topologies for the outdated Gromos87), and the quality of the 
topologies is generally very low.  The resulting topologies require significant 

> N.B:  I am using the OPLSAA force field .I also have the files in MDL MOL2 version which do not contain the LIG residue appearing in the PDB file. So maybe using PRODRG on the MOL2 might solve the problem?

I don't understand this.  PRODRG will be of no use here since you are using 
OPLS-AA, and if there is no ligand, then why do you need some external program 
to build a topology?



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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