VMD-L Mailing List

From: Jan Saam (saam_at_charite.de)
Date: Wed Jan 31 2007 - 14:14:01 CST

Javaria,

this will do partially.
You can load a xbgf file as base molecule in paratool. This will cause
VMD to display all bonds the way you defined them. But you still have to
define which internal coordinates (bonds, angles, dihedrals) you want to
use for your force field of the molecule. You can manually define them
or simply autogenerate them:
Edit-->"Internal Coordinates"-->"Autogenerate internal coordinates"
This will generate all bonds (based on what's displayed in VMD i.e. what
came with the xbgf) and all angles and dihedrals that can be constructed
from these bonds.
For this set of internal coordinates you will generate force constants.

Jan

Javaria Ahmed schrieb:
> Dear Jan
>
> I have stored my pdb file with psf data loaded as xbgf in molefacture. Will
> this do? (now the geometry is defined with bonds, dihedrals etc)
>
> Javaria
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu on behalf of Jan Saam
> Sent: Mon 1/29/2007 6:00 PM
> To: Javaria Ahmed
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Regarding paratool
>
> 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
>>
>>
>>
>
>
>
>
>
>
> 

-- 
---------------------------
Jan Saam
Institute of Biochemistry
Charite Berlin
Monbijoustr. 2
10117 Berlin
Germany
+49 30 450-528-446
saam_at_charite.de