[gmx-users] tpr without top-file

[Anton Feenstra]

Peter Zoon wrote:

> sounds like a good plan, but would this also work for a somewhat more 
> complicated system?
> my system looks more or less like this:
> 
> thread= napthalimide-(CH2)12-succinamide-CH2-C-(phenyl)2
> 
> the macrocycle consists of a coupleof phenyl rings bonded together via amide groups.
> 
> I think most of the atoms are in ffgmx.n2t so I'll give it a go.

Alternatively, it shouldn't be a problem to write your own program (or perl
or awk script), that generates a dummy topology, with the proper atom names
(which you can read from the .gro file) and only bonds for the connectivity.
For the bonds, you'll probably want to parse those out of the topology file
you used in your 'other' md program. You'll need to add in fake atom types
and fake parameters for the bonds as well, since grompp requires them.

I once wrote an amber2gromacs topology converting script (in awk...), which
you may want to use as a template. It has the code to write topology files.
It should be in the contributions section, otherwise it'll be in the mail
list archives somewhere. If that fails, ask me.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
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