[gmx-users] merging and renumbering topology atoms

[Anton Feenstra]

christoph.nimptsch at uni-tuebingen.de wrote:

> Hello,
> 
> I created a ligand with PRODRG and now I want to define distance constraints.
> As far as I know gromacs expects all atoms in one file. 
> So, my idea was to renumber the atoms in the topology DRGGMX.ITP and include
> it in protein.top.
> 
> Is there any programm, that can do the renumbering? Or is there a switch in
> PRODRG, which forces the atoms to be numbered from a certain number?

A while ago I posted some scripts to the list that do exactly that (if you
know how to write 'awk' and how the .top files are organized, it is surprisingly
simple to do!). I may also have put them on the contributions page on the
website. I don't have them handy here, so you are probably fastest off by
locating them yourself in the archives (try 'renumber') or on the website.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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