[gmx-developers] Generating topologies and assigning hydrogens

Anton Feenstra feenstra at few.vu.nl
Wed Jun 22 16:02:39 CEST 2005

Michael Shirts wrote:
>>The code analyzes hydrogen bonding (networks) in the structure to assign
>>the most probable protonation state, and seems to do a proper job there.
>>Indeed, it has to do with more than just topology assignment. Other than
>>that, I've never even looked at this part of the code, so can't help you
> Ah, that makes sense.  The problem is, if the hydrogens are already in
> place (for example, if you are taking coordinates from a pdb output by
> another program), it causes the die with an error, because it tries to
> add in hydrogens that are already there.
> Perhaps there is some hidden flag (because I don't see it documented
> in pdb2gmx) that allows you to avoid this?  Or does this need to be
> added so that it will accept the pdb "as is" instead of trying to
> protonate?

I'm not aware of such an option, but removing the .hdb file (or specific 
entries) will work (although rather inconveniently...). It would not be 
too hard to code it in, but IIRC, there is also a major overhaul 
(planned or going on already?) in the topology parsing and 
pre-processing scheme for the next (or after?) gromacs version. One of 
the specific issues is that the whole .hdb file is redundant, and the 
information can also be inferred from the topology. That could make the 
mechanism generic and allow it to generate any type of missing atoms 
(alhough limited in how many you could sensibly generate in this 
fashion), and not only hydrogens.



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|  _   _  ___,| K. Anton Feenstra                                     |
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