[gmx-users] pdb2gmx for non-proteins

[Christoph Freudenberger]

Hi there,

I'm thinking about how to generate the top's for tripodal
scaffold-molecules bearing different substituents:

     R1
       \
        Scaf--R3
       /
     R2

The scaffold is an aryl-ring and R1-3 should be arbituary
substiutents.
I wonder if it is possible to add rtp-entries for Scaf and
the R's and let pdb2gmx do the job.
Is pdb2gmx able to handle non-chain-like molecules?
How are the links recognized? Automaticly (e.g. by distance)
or do I have to define them?
Is it vital to have the atoms in the same sequence in the
pdb and the rtp?

thanks
-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785