Re: [AMBER] RED vIII for Amber

From: Nash, Anthony <>
Date: Sun, 20 Dec 2015 17:23:28 +0000

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.

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.


On 14/12/2015 07:50, "Nash, Anthony" <> 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
>On 14/12/2015 07:42, "Karl Kirschner" <> 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
>>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.
>>On Sun, Dec 13, 2015 at 10:41 PM, Nash, Anthony <> wrote:
>>> Hi all,
>>> With the RED server having gone down, I know a link to the older
>>> scripts (vIII) had been publicised in this Amber community. After
>>> through the various scripts, it seems relatively easy to set up on a
>>> system with access to Gaussian. However, after carefully going through
>>> only .pdf tutorial for vIII I didn't find anything to do with
>>> 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
>>> list of atoms which would not contribute to the calculation of point
>>> charges (essentially capped ends to an amino acid backbone). Was this
>>> of the differences between III and IV?
>>> I©öm getting the feeling I©öll need to move back onto Antechamber.
>>> Thanks
>>> Anthony
>>> _______________________________________________
>>> AMBER mailing list
>>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 mailing list

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Received on Sun Dec 20 2015 - 09:30:03 PST
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