[gmx-users] pdb2gmx for non-proteins

[Anton Feenstra]

Christoph Freudenberger wrote:
> One more thing about rtp-entries:
> 
> Is it possible to make dummies in the building blocks?
> Where and how are they defined?

Don't think so. There is code in pdb2gmx that generates them for
certain atom 'constellations' (the -dummy hydrogen/aromatic options),
and code in grompp that adds in appropriate parameters (since pdb2gmx
only parses the topology itself and not the parameters).

It may be that by now (it's been some time since I did coding on
pdb2gmx), the .rtp parsing is as generic as the other topology stuff,
so you could add anything you like, but I'm not sure. It wouldn't
be too hard to add, but you need to know how and where.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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