I too was able to register, and got as far as Anthony did. I too have tried many times to contact the authors of the site, with no luck. But I think the link to the site (
http://upjv.q4md-forcefieldtools.org/index.php) is new - I don't recall the 'upjv' from back in the day.
Fingers crossed
Steve
-----Original Message-----
From: Nash, Anthony [mailto:a.nash.ucl.ac.uk]
Sent: Sunday, December 20, 2015 12:23 PM
To: AMBER Mailing List
Subject: Re: [AMBER] RED vIII for Amber
I managed to get through to the RED server, and even register (even got the email). Yet from the homepage the PyRED (REDSD) doesn't load.
http://upjv.q4md-forcefieldtools.org/index.php
Anyone had any news with regards to this service? I emailed several authors only two weeks ago and I haven't had a single reply.
Thanks
Anthony
On 14/12/2015 07:50, "Nash, Anthony" <a.nash.ucl.ac.uk> wrote:
>Many thanks Karl,
>
>That's exactly what I've been looking for. I recall it was a parameter
>in the project.config file for red vIV, but I've yet to be able to find
>whether this was possible in vIII.
>
>Thanks again
>Anthony
>
>
>On 14/12/2015 07:42, "Karl Kirschner" <k.n.kirschner.gmail.com> wrote:
>
>>Hi Anthony,
>>
>> I believe the way to do this is to manually include the following
>>line (as an example) in your RED input p2n file:
>>REMARK INTRA-MCC 0.2 | 3 | K
>>
>>The 0.2 is the charge that you want to constrain atom #3 to have
>>during the fitting process. You can include as many of these lines as
>>the number of atoms that you want to keep the partial atomic charge
>>constrained to.
>>
>>Bests,
>>Karl
>>
>>On Sun, Dec 13, 2015 at 10:41 PM, Nash, Anthony <a.nash.ucl.ac.uk> wrote:
>>
>>> Hi all,
>>>
>>> With the RED server having gone down, I know a link to the older
>>>version scripts (vIII) had been publicised in this Amber community.
>>>After looking through the various scripts, it seems relatively easy
>>>to set up on a local system with access to Gaussian. However, after
>>>carefully going through the only .pdf tutorial for vIII I didn't
>>>find anything to do with restraining the calculation of point
>>>charges to certain regions of an amino acid.
>>>If I
>>> recall correctly, the defunct online service allowed you to provide
>>>a project and system file. One of these files enabled the user to
>>>specify a list of atoms which would not contribute to the
>>>calculation of point charges (essentially capped ends to an amino
>>>acid backbone). Was this one of the differences between III and IV?
>>>
>>> Iım getting the feeling Iıll need to move back onto Antechamber.
>>>
>>> Thanks
>>> Anthony
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>>--
>>Karl. N. Kirschner, Ph.D.
>>Research Associate
>>Bonn-Rhein-Sieg University of Applied Sciences Grantham-Allee 20,
>>54757 Sankt Augustin, Germany
>>_______________________________________________
>>AMBER mailing list
>>AMBER.ambermd.org
>>http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Dec 20 2015 - 16:00:03 PST
