[gmx-users] pdb2gmx for non-proteins

[Osmany Guirola Cruz]

On Tuesday 15 April 2003 13:00, Christoph Freudenberger wrote:
ss> 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