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 - 13:30:02 PDT
