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 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
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Received on Thu Oct 22 2015 - 13:30:04 PDT
