VMD-L Mailing List

From: Jan Saam (jan.saam_at_charite.de)
Date: Mon Jan 29 2007 - 11:00:14 CST

Javaria,

you have to tell Paratool which bonds you want to have defined or at least
request a distance based autodetection. This is done in the Internal
Coordinates window.

Jan

---------------------------
Jan Saam
Institute of Biochemistry
Charite Berlin
Monbijoustr. 2
10117 Berlin
Germany

+49 30 450-528-446
saam_at_charite.de

> Hi
>
> My question is regarding paratool;
>
> Paratool accepts pdb file as input of base molecule, my molecule is an
> inorganic diatomic crystal. (I want to load a base molecule of lets say
> 14
> atoms)
>
> How will paratool parameterize a molecule without knowing atom
> connectivity
> (i.e psf file), that what is its crystal structure, how are atoms
> connected, which atoms are connected and which are not?
>
> And how can I edit such a structure in Molefacture.
>
> Regards
>
> javaria
>
>