Dear Amber users,
I personal copy of the RED3 software would be downloaded from the
following link:
https://drive.google.com/open?id=0B5XRc5OC2AOKN1BZWmZ1UUFwaEk
Greeting,
Hector.
> Dear Dr Baldoni,
>
> If you have time, could you also send me a copy of RED3 please?
>
> Thanks a lot!
>
> Regards,
> Jia
>
> On Thu, Oct 22, 2015 at 5:29 PM, Hector A. Baldoni <hbaldoni.unsl.edu.ar>
> wrote:
>
>> 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  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
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> --------------------------------------
>> Dr. Héctor A. Baldoni
>> Profesor Adjunto
>> Departamento de QuÃmica
>> Ãrea de QuÃmica 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
>> --------------------------------------
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
--------------------------------------
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 Fri Oct 23 2015 - 10:30:03 PDT
