Hi,
Last monday I shared, offline, a personal copy of the RED3 version with
Professor Matej Repic. I sent to copy to the amber mailing list but the
message was stoped and rejected by the list moderator.
Greeting,
Hector.
> Many thanks Jason,
>
> A kind reader of this distribution just sent me a link to a rescued copy
> of the packaged R.E.D. Server scripts. I’ve just emailed my IT guys who
> run the clusters at UCL asking them kindly for their support in setting
> up
> our own R.E.D server. Hopefully I can continue using a service that I am
> familiar with but also on home turf (where I can see the full output of
> the Gaussian .out/.log files).
>
> Thanks for those alternative suggestions, with any luck I won’t need to
> use them but if I do I now know where they are.
>
> Thanks
> Anthony
>
>
> Dr Anthony Nash
> Department of Chemistry
> University College London
>
>
>
>
>
> On 22/10/2015 21:17, "Jason Swails" <jason.swails.gmail.com> wrote:
>
>>I have no idea when or even if q4md-forcefieldtools will come back up,
>> and
>>the R.E.D. developer that frequents the Amber mailing list has not
>>responded to any of these questions. That leads me to suspect that
>> maybe
>>whatever outage is affecting the website is also affecting his email
>>service (but that is pure speculation based on absolutely no insider
>>information).
>>
>>So you know as much as anybody else when R.E.D. Server might come back
>>(which is one of the risks of making a web-only service an integral part
>>of
>>a workflow). There are two main open questions to which I don't know
>> the
>>answer (and I don't know anybody that does, although I haven't asked):
>> (1)
>>when will the RED website be restored? and (2) is the outage even
>>temporary
>>at all?
>>
>>On the bright side, if you go to q4md-forcefieldtools.org, you (or at
>>least
>>I) get a plain page that says "It works! but there's no content yet".
>> So
>>maybe it's on its way to coming back up (or maybe not, I don't know).
>>
>>If someone has an old copy of the perl scripts that they *did* release
>>back
>>in the day, the license permits redistribution (I might have them
>>somewhere, but I have no idea where, and I probably deleted them).
>>Otherwise, it might be time to start looking for alternatives. A few
>>ideas
>>here:
>>
>>- A combination of antechamber and prepgen could do the trick (see
>>http://ambermd.org/tutorials/basic/tutorial5/)
>>- You could read up on how to use resp directly (of course you don't get
>>the auto-detection of atom equivalencing and multiconformational fits --
>>those would have to be done by hand)
>>- I believe mdgx has some RESP fitting functionality that Dave Cerutti
>>used
>>to derive charges for ff14ipq. It might do the same RESP strategy for
>> the
>>Cornell family of FFs as well (I believe that Dave documented his code
>> in
>>the manual).
>>
>>On the bright side, a workflow using any of those alternatives would be
>>immune to any future DDoS attacks on Rutgers internet servers that have
>>brought our website down a few times this past year :).
>>
>>All the best,
>>Jason
>>
>>On Thu, Oct 22, 2015 at 3:36 PM, Nash, Anthony <a.nash.ucl.ac.uk> wrote:
>>
>>> Just to follow up on this, has anyone heard/read/found some news with
>>> regards to RED? I was hoping it would be backup by now or at least a
>>> temporary Œconstruction¹ page in place.
>>>
>>> Regards
>>> Anthony
>>>
>>>
>>>
>>> Dr Anthony Nash
>>> Department of Chemistry
>>> University College London
>>>
>>>
>>>
>>>
>>>
>>> On 19/10/2015 08:21, "Repic Matej" <matej.repic.epfl.ch> wrote:
>>>
>>> >Dear Amber users,
>>> >
>>> >Does anyone have a backup of standalone RED-tools (Ante-RED.pl and
>>> >RED-Vx.x.pl) and would be willing to share?
>>> >
>>> >Thanks,
>>> >
>>> >
>>> >------------------------------------------------------
>>> >Dr. Matej Repic
>>> >Ecole Polytechnique Fédérale de Lausanne
>>> >Laboratory of Computational Chemistry and Biochemistry
>>> >SB - ISIC Â LCBC
>>> >BCH 4108
>>> >CH - 1015 Lausanne
>>> >------------------------------------------------------
>>> >_______________________________________________
>>> >AMBER mailing list
>>> >AMBER.ambermd.org
>>> >http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>>--
>>Jason M. Swails
>>BioMaPS,
>>Rutgers University
>>Postdoctoral Researcher
>>_______________________________________________
>>AMBER mailing list
>>AMBER.ambermd.org
>>http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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>
--------------------------------------
Dr. Héctor A. Baldoni
Profesor Adjunto
Departamento de Química
Área de Química General e Inorgánica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
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Received on Thu Oct 22 2015 - 15:30:04 PDT
