Subject: assigning atom types

From: Ingo Mugge <[email-masked]>
Date: Fri, 10 Jul 1998 17:15:05 -0500 (CDT)

Dear CCL'ers,

I am looking for software that is able to automatically
and reliably determine the number of hydrogen atoms attached to heavy 
atoms given in a reasonable conformation in a PDB file or
any other format and assign atom types of some sophistication. 
Considering the pH and pKa dependence of 
protonation states I am asking only for potentially present hydrogens 
like in an imidazole ring where one, the other, or both nitrogens might 
be protonated in proteins, meaning that both imidazole nitrogens 
could be assigned the same atom type. On the other hand, however, 
if you have for instance pyrrol rings in a porphyrin the program 
should be able to distinguish between those nitrogens that have 
hydrogens attached and those that don't and assign different atom types
to them. So, I guess I am more interested in a program that recognizes the
right atom types of the heavy atoms (especially in heterocycles) 
leaving it open if they are really protonated or not.

I realize that this question was asked before in CCL at least once
about 4 years ago but I did not find a good answer (Sorry if I did
not search the archives thoroughly enough). I know some
programs that almost do it correctly but still ask for manual 
intervention at some point.

Thank you very much for your help.

Ingo Mugge 
[email-masked]