[gmx-users] PRODRG topology

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 4 17:29:04 CEST 2011

Marzinek, Jan wrote:
> Dear Gromacs Users,
> I used PRODRG server in order to obtain the topology file for my 
> molecule (52 atoms with all hydrogens). However, server generated 
> Gromacs topology which involves 47 atoms (for PDB file with 
> polar/aromatic hydrogens). Whether I will use the pdb file with missing 
> 4 hydrogen that wont be a good apporximation. How to overcome this?

The Gromos96 force fields are united-atom force fields and may not use all the H 
atoms your input coordinates did.  If you suspect some issue with protonation 
state, PRODRG can be forced into certain protonation with the ADDHYD or DELHYD 
keywords.  Be advised, of course, of the usual caveats regarding the quality of 
PRODRG topologies:




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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