VMD-L Mailing List

From: Javaria Ahmed (javah_at_itn.liu.se)
Date: Mon Jan 29 2007 - 16:22:17 CST

Hi

Jan, Paratool main screen is not listing any defaultly uploaded topology
file.
How can I check , why is that? and how to correct it?

Best Regards,
Javaria

-----Original Message-----
From: Jan Saam [mailto:jan.saam_at_charite.de]
Sent: Mon 1/29/2007 5:56 PM
To: Javaria Ahmed
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: Regarding paratool, assign atom types

Hi Javaria,

you get the charmm types only if you have loaded the corresponding CHARMM
topology and parameter files that contain the VDW parameters for Zn and O.
Paratool should actually load a default CHARMM topology file which
contains the parameters for ZN and O. The file should be listed in
Paratool's main screen.

Jan

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

+49 30 450-528-446
saam_at_charite.de

>
> Hi
>
> I am parameterizing a ZnO molecule using Paratool and following the steps
> mentioned in Paratool documentation. While assigning atom types, when I
> proceed to - Choose Type - step, I only get to choose atom types from
UFF.
>
> I want to choose atom types Zinc Ion - ZN and Ester Oxygen - OS from
> charmm
> force fields instead of choosing some atom type from UFF.
>
> How do I get those atom types and their parameters in selection?
>
> Regards,
> Javaria
>