Re: [AMBER] RED vIII for Amber

From: Nash, Anthony <a.nash.ucl.ac.uk>
Date: Mon, 14 Dec 2015 07:50:56 +0000

Many thanks Karl,

Thats exactly what Ive been looking for. I recall it was a parameter in
the project.config file for red vIV, but Ive 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?
>>
>> Im getting the feeling Ill need to move back onto Antechamber.
>>
>> Thanks
>> Anthony
>>
>>
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>>
>
>
>
>--
>Karl. N. Kirschner, Ph.D.
>Research Associate
>Bonn-Rhein-Sieg University of Applied Sciences
>Grantham-Allee 20, 54757 Sankt Augustin, Germany
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Received on Mon Dec 14 2015 - 00:00:04 PST
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