I can't yet say anything about the real-life behavior of ligands, but
proteins themselves seem to work much better when you do the charge
derivation with accounting for the different phases. Hopefully we'll have
data on an assortment of small molecules soon; I think that you ligands are
near the upper end of what I've done in mdgx so far, so perhaps not the
best case for you to get started with, but it behooves me to make
additional functionality like a script fro breaking molecules into smaller
chunks that can then be submitted to these REsP-like derivations, or to
link mdgx with a quantum package that can break quantum systems into chunks
and then stitch the results back together.
Dave
On Fri, Feb 26, 2016 at 5:57 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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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>
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Received on Fri Feb 26 2016 - 08:00:06 PST
