Hector:
This may be a fair amount of work, but I'm sure the community would appreciate it...would you mind describing how one next installs RED? And maybe even a primer on using it? I know that's asking a lot...
Steve
-----Original Message-----
From: Hector A. Baldoni [mailto:hbaldoni.unsl.edu.ar]
Sent: Friday, October 23, 2015 1:12 PM
To: amber.ambermd.org
Cc: xujia.ruc.gmail.com
Subject: Re: [AMBER] RED-tools
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
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>> >>>
>> >>
>> >>
>> >>
>> >>--
>> >>Jason M. Swails
>> >>BioMaPS,
>> >>Rutgers University
>> >>Postdoctoral Researcher
>> >>_______________________________________________
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>> >
>> > _______________________________________________
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>> > 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 Sun Oct 25 2015 - 16:00:03 PDT
