[gmx-users] Polar Hydrogen missing using PRODRG
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
The King's Buildings
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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