Dear Professor Graham,
I apologize for not being able to carried out your order but if you has
never installed or used R.E.D., please forget about it and stay with
antechamber that (I think) it is more friendly. However, some related
papers are in the following links:
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.465.154&rep=rep1&type=pdf
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
http://ambermd.org/tutorials/advanced/tutorial1/
Best regards,
Hector.
> 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
>>> >>> 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 QuÃÂmica
>>> ÃÂrea de QuÃÂmica 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 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 - 20:00:03 PDT
