[Chimera-users] Errors applying AddCharge to PDB files with non-Chimera protonation

[Eric Pettersen]

Hi Matthias,
	I am unaware of any definitive web page detailing the PDB’s hydrogen naming conventions.  What I have usually done is to simply take a PDB entry determined by NMR that has the standard residues I care about (e.g. 1mtx) and see what the hydrogen names are.  You could also probably extract the names from the appropriate part of the PDB’s Chemical Component Dictionary <http://wwpdb.org/data/ccd>.
	How did Protoss protonate the N in the 2.A ALA?  That ALA is not in fact N-terminal and therefore should only have an ‘H’ attached.  Did Protoss treat it as N-terminal and add 3 protons?  If so, the names should at least be H1/H2/H3 and not H/H2/H3.  If the latter, you should probably alert the Protoss people that they are using non-standard N terminus hydrogen names.  They’d probably appreciate knowing that they are outputting non-standard names.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Sep 12, 2018, at 6:48 AM, Matthias Bal <matthiascbal at gmail.com> wrote:
> 
> Hi,
> 
> I have a large amount of PDB files which need explicit hydrogens for MD and quantum calculations. To go beyond Chimera's AddH function, I've tried using the Protoss tool among others. Trying to add charges (AMBER ff14SB) using Chimera to PDB files protonated in this way leads to errors regarding non-standard atom names in standard residues.
> 
> For example, the protonated PDB case 1amw gives the following errors in the Reply Log:
> 
> > Non-standard atom names:
> >     ALA H (ALA 2.A H)
> > Total charge for #0: -12.939
> > The following residues had non-integral charges:
> >     ALA 2.A 0.4009
> >     LYS 102.A 0.66
> > Correct charges are unknown for 1 non-standard atom names in otherwise standard residues
> > Charges of 0.0 were assigned to the unknown atoms
> 
> I know the suggestion of the help page on AddCharge is to remove the hydrogens and re-add them using AddH since they are often the problem, but that's not really an option in this case. Is there an overview somewhere of all the different PDB hydrogen naming conventions (like a more recent version of https://www.ics.uci.edu/~dock/pdb2pqr/programmerguide.html <https://www.ics.uci.edu/~dock/pdb2pqr/programmerguide.html>) and how they relate to what Chimera/Amber is using? And is there a way to script the conversion to treat files in batches?
> 
> Thanks a lot,
> Matthias
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