Kavin,
> The submit/download service appears to work fine (or I don’t know
> what I’m missing) on Chrome (for Mac). I’m guessing the applets are
> only for visualisation?
Yes
Java applet + PDB file
-> Display molecule orientation, atom names, indexes + conformation
(optimized geometry or input structure)
Java applet + mol2/mol3 file
-> Display atom names, atomic charges, atom types + conformation
(optimized geometry)
regards, Francois
> On 26 Feb 2016, at 09:10, FyD
> <fyd.q4md-forcefieldtools.org<mailto:fyd.q4md-forcefieldtools.org>>
> wrote:
>
> Dear Kavin,
>
> You’re quire right about R.E.D. Server - I was being blind and led
> astray by the numerous “Cannot run Java applet” security prompts and
>
> Concerning security & Java:
>
> I just installed JRE Version 8 Update 73 under my linux box :
> https://www.java.com/en/download/
> Create a link for firefox (my box is 64 bits):
> ln -s /usr/java/jre1.8.0_73/lib/amd64/libnpjp2.so
> labo2:/usr/lib/mozilla/plugins/libnpjp2.so
>
> I run the "control" utility of JRE and I select the "Security" tab:
> /usr/java/jre1.8.0_73/bin/jcontrol
>
> 1) Decrease the security from "VeryHigh" to "High"
>
> 2) Add two sites in the Exception Site List:
> http://upjv.q4md-forcefieldtools.org -> web server
> http://cluster.q4md-forcefieldtools.org -> cluster
>
> Both sites should work with firefox.
> It does _not_ with chromium from what I understand.
>
> When connecting to the cluster machine (through for instance the
> Download service
> http://upjv.q4md-forcefieldtools.org/REDServer-Development/download.php) the
> _first_ time you connect you will have to provide _twice_ your
> login/password (first for the web server and second for the cluster).
> Then when running a java applet from your work space you might have to
> (i) Activate and (ii) Run the Java Applet and then (iii) provide again
> your login/password... This is tedious but it works fine once you
> passed all these steps...
>
> From my tests the Opera browser can run java applets from the web
> server, but not from the cluster (because login/passwd are required).
>
> So by now, I only use Firefox when I want to display Java Applets from
> my space work in the cluster of q4md-forcefieldtools.
>
> I hope this helps.
> regards, Francois
>
>
> On 19 Feb 2016, at 17:24, David A Case <david.case.rutgers.edu> wrote:
>
> On Fri, Feb 19, 2016, Abelak, Kavin wrote:
>
> I find myself needing to derive charges for some non-standard
> ligands. I’ve had a brief search through the archives
> and tutorials, and keep getting referred to tutorial A1
> (http://ambermd.org/tutorials/advanced/tutorial1/section1.htm). Is this
> still the currently accepted method for running charge derivations using
> Gaussian? I only ask as it is dated 2008 and cites Amber 10 (and older).
>
> The standard charge derivation procedure has not changed since forever (i.e.
> since the early 1990's). So the tutorial should still be OK, but be sure to
> read the caveat there (in bold type).
>
>
> Another related question is: are there other streamlined methods
> (similar to R.E.D Tools) that anyone can suggest?
>
> Why not use R.E.D. Tools itself? That is the most popular way, as far as I
> can tell. They maintain a large-ish database that may already have your
> ligand, or something close to it.
>
> ....dac
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Fri Feb 26 2016 - 03:00:12 PST
