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