Summary of hydrogen adding programs

M. L. Dodson bdodson at BEOWULF.UTMB.EDU
Fri Jul 15 14:10:44 EST 1994


A couple of weeks ago I posted a request for pointers to programs which could
add standard geometry hydrogens to a PDB file.  The posting is repeated 
below, followed by the responses.  This followup is presented in case 
someone else needs this kind of information.


Hello all,
I am looking for a particular kind of software.  I need to be able to
add hydrogens to PDB files (in standard geometry).  I expect to have to
identify what _kind_ of atoms are in the molecule.  I can do this, but in
a very cumbersome fashion, in amber.  This is in preparation for a mopac
run to get partial charges.  If the software had the ability to convert
between cartesian and internal coordinates with a simple option choice,
it would be even better :)  If anyone has a pointer to (preferably) non-
commercial software that has this capability, please let me know.  Unix
is preferred, although Mac or PC is not out of the question.  VMS does me
no good unless it is in source form.
Bud Dodson


Ton Rullmann <rull at> and
Dan R. Wilson <drwilson at>	
made me aware of the program, Babel, from 
Pat Walters <pat at> and 
Matt Stahl <matt at> 
at the University of Arizona.  This was the program that I eventually came
to use.  Based on my, admittedly limited, experience with the program, I am
quite impressed.  It did exactly what I wanted, right down to doing the
coordinate conversion (which is its main reason for existence). Babel is 
avialiable via annonymous ftp from in pub/Babel

Clemens Vonrhein <vonrhein at> suggested that XPLOR was
able to do this easily.  Unfortunately, I don't have ready access to XPLOR.

Christoph Weber <cweber at> 
suggested that Peter Guentert <guentert at> had a utility 
(part of the DIANA suite) that would add hydrogens to pdb and a number of 
other coordinate files. It's called COFIMA for Coordinate File Manipulation.
I found out about Babel just as I was going to get more information on this

David G. Rhodes <rhodes at>
suggested that QCPE had a program which could do this.  As in the case of 
the COFIMA program, I got Babel and evaluated it before I could follow up.

Also, along vaguely the same line, there is HBPLUS by Ian McDonald et al.  
Contact mcdonald at
This is a hydrogen bond calculation program.  It calculates position, etc. 
for polar hydrogens.  Email for a confidentiality agreement.

Thanks to all who responded.
Bud Dodson
M. L. Dodson                                bdodson at
409-772-2178                                FAX: 409-772-1790

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