[gmx-users] Polar Hydrogen missing using PRODRG

Jennifer Williams Jennifer.Williams at ed.ac.uk
Wed Oct 13 19:02:34 CEST 2010


I am trying to get a .itp file for a simple molecule (Ibuprofen). This  
contains a COOH group.

THe problem is that PRODRG removes the polar hydrogen of the COOH from  
the .pdb file and generates a .itp file without it.

I am not concerned about the other aromatic hydrogens but I really  
need the polar hydrogen modelled explicitly.

Is there a fix for this within PRODRG?

I know I can use pdb2gmx to add hydrogens but the residue names of the  
pdb file are not recognized by the existing forcefields so I usually  
bypass using pdb2gmx.



Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
Sanderson Building
The King's Buildings
Mayfield Road
Edinburgh, EH9 3JL, United Kingdom
Phone: ++44 (0)131 650 4 861

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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