Thanks for the details and comprehensive instructions Francois.
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?
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 - 03:00:06 PST
