VMD-L Mailing List

From: Jan Saam (saam_at_charite.de)
Date: Fri Jun 15 2007 - 11:11:10 CDT

Hi Michel,

thanks for your note!

Since I have been busy with other things I haven't had time for any
serious Paratool developing nor to write the paper. Before the paper I
still want to include a few very crucial features to Paratool and make
it at least a bit more understandable and user friendly.
I wonder if actually ever anybody other than me was able to do some
thing useful with Paratool. My assumption is that everybody who tried it
got stuck at one or the other point and gave up.

I currently have a paper under review where Paratool is mentioned
because the work uses parameters that were generated with Paratool. I am
confident that the paper will be accepted (I hope, I hope!).

Maybe for now you could use this reference (Saam, et al. " Molecular
dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen
access channels*",* PNAS 2007).

I know that this deprives the other Paratool-contributors of their
credits but since I am reponsible for >95% of Paratool I think this is
ok for now. Of course this will only be a temporary solution.

Regards,
Jan

L. Michel Espinoza-Fonseca schrieb:
> Hi Jan,
>
> Now that I saw this posting, something came to my mind: do you already
> have a paper describing paratool? It is indeed nice to have a tool
> that makes the parametrization process much easier, but I think it'll
> be fair (for you and the people involved in its development) to be
> able to cite it somehow.
>
> Cheers,
> Michel
>
> 2007/6/11, Jan Saam <jan.saam_at_charite.de>:
>> Hi Vivek,
>>
>> I must admit that this is a flaw in the GUI design. There are just too
>> many elements in that window and it cannot be resized. I will fix
>> this in
>> a later version of Paratool. Until then the only advice I can give
>> you is
>> to use a higher screen resolution.
>> Anyway I recomment using VMD 1.8.6 since some Paratools bugs (and other
>> bug, too) are fixed in the new version.
>>
>> Jan
>>
>> ---------------------------
>> Jan Saam
>> Institute of Biochemistry
>> Charite Berlin
>> Monbijoustr. 2
>> 10117 Berlin
>> Germany
>>
>> +49 30 450-528-446
>> saam_at_charite.de
>>
>>
>>
>>
> 

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