[gmx-users] merging and renumbering topology atoms
feenstra at chem.vu.nl
Tue Oct 28 09:01:07 CET 2003
christoph.nimptsch at uni-tuebingen.de wrote:
> 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.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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