[gmx-users] Sigh . . . Protonating PDB for PRODRG

Marc Charendoff mcharend at sbcglobal.net
Tue Aug 15 02:51:37 CEST 2006

Hey all, 

I'm trying to import energy minimization files into
VMD to view and I'm getting some errors. First I note

	•	small molecule pdb file shows a total of 48 atoms
	•	my new molecule topology (*.itp file, and *.gro
file) show 22 atoms, which I thought were non-H atoms
	•	My tally of non-H atoms show 21 non-H atoms (16
C's, 4 O's, and 1 N)-What's going on here?
	•	My *.ndx file shows 22 atoms

I ran grompp and make_ndx using the small molecule gro
and itp files generated by PRODRG. Obviously I lost
H's when processing the original pdb file in PRODRG
(RTM). When reviewing PRODRG website I saw one can use
the ADDhyd [atomname] to the input drawing file, but
seeing as  HETATM already designates the hydrogen this
doesn't make sense. In any case, how do I add more
than one H to an atom (e.g. methyl group CH2, CH3)?
Where do I place these statements in the file? Last,
if the input file to PRODRG is fixed, will this allow
VMD to run? Any specific examples or guidance on how
to protonate atoms in .pdb files would be greatly



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