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

[Matthias Bal]

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) 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180912/4c70dab6/attachment.html>