Dear Marek,
In short to try to make it clear ;-)
The RED Python or PyRED program is object oriented (compared the
R.E.D. III.x tools or even to R.E.D. IV) and many algorithms are I
think robust...
- this painful P2N file format is retired, and replaced by the PDB
file format; i.e. Ante_RED & RED are merged into a single program: PyRED
- the execution of PyRED is controlled by using a system of keywords
defined in two configuration files (the source code does not need to
be modfied anymore).
- chemical equivalencing (CE): you can compare Antechamber (ver. from
AmberTools 12; did not test the last version) vs REDServer Dev/PyRED.
The algorithm, that Fan has developed is impressive for complex cases
such as functionalized CNTs & fullerenes. Ante_RED 1.x does not really
handle CE, and Ante_RED 2.0 (algo is too basic) is limited like the
tested version of Antechamber.
- atom typing for whole molecules, but also for molecular fragemnts
_with open valencies_! look at Antechamber again here.
- fragment fusions to solve bugs in LEaP at chiral centers and more;
see the F-90 REDDB project: what if all the possible combinations
could be automatically generated (because they are all useful): this
is the idea...
- handle all the elements of the periodic table, with complex
approaches for bioinorganic complexes such as the broken symmetry
procedure, when an active site contains several 'connected' metal
centers for instance
- user defined options as suggested by a former reviewer
- automatic procedures to generate amino acid and nucleotide fragments
etc... see
http://q4md-forcefieldtools.org/REDServer-Development/news.php
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
So in this context R.E.D. III.x tools or even to R.E.D. IV can still
be used (this is why they are still available) but they are...
limited. Our group is small (not easy to work without stable funding):
we cannot maintain the R.E.D. III.x tools & R.E.D. IV; so their
developments are simply stopped. RED IV ? the source code is just a
battle field: we have at least four versions of this code, and the
last one is even not the one, that is interfaced by the server: this
is why we decided to follow an object oriented approach using the
Python programming language and to develop a totally new code from
scratch: PyRED.
We just released R.E.D. Server Development May 2014, which is finally
open to all, and not only to academics (Nov 2013). This server
interfaces PyRED version May 2014.
Next step: Fan is going to defend his thesis, and in six months or so:
release of the PyRED Nov 2014 version at R.E.D. Server Dev.
and Yes we will distribute PyRED as a standalone program under the GNU
General Public License. For that we need to write a real manual; this
is on our todo list with may be writing papers ;-)
regards, Francois
> it seems that in your R.E.D. Download section there is still available
> only "RED-III.52-Tools" (from September/October 2012) represented mainly by
> "RED-vIII.52.pl" script.
>
> Is there any hope that the newest version of the tools represented
> by "PyRED" Python program or at least RED-IV tools will be ever available
> for download and for custom usage on our own hardware ? Or the RED-III.52
> tools
> was the last one and who wants to use the more actual tools is forced to
> use it
> only through your web interface/your servers ?
> Dne Mon, 05 May 2014 13:00:11 +0200 FyD <fyd.q4md-forcefieldtools.org>
> napsal/-a:
>
>> Dear Amber Users,
>>
>> In the context of a joined French-USA research project between the
>> Universite de Picardie - Jules Verne and the Sanford|Burnham Medical
>> Research Institute I am pleased to announce the release of the May
>> 2014 version of the RED Python program, or PyRED, interfaced by R.E.D.
>> Server Development at q4md-forcefieldtools.org:
>>
>> http://q4md-forcefieldtools.org/REDServer-Development
>>
>> R.E.D. Server Development is a service designed to generate force
>> field parameters and build force field libraries for new
>> molecules/molecular fragments. This Internet site provides the
>> software and hardware resources required for the generation of AMBER
>> and GLYCAM type empirical force fields, that can be used by
>> computational biologists involved in force field based structural
>> studies. CHARMM and OPLS force fields can also be targeted by applying
>> user-defined options.
>>
>> All researchers from the academic world and from private laboratories
>> can use R.E.D. Server Development, and registration to use R.E.D.
>> Server Development is not mandatory.
>>
>> PyRED was presented at the 247th ACS National Meeting in Dallas (TX,
>> USA) last March 2014:
>>
>> http://abstracts.acs.org//chem/247nm/program/view.php?pub_num=277&par=COMP
>>
>> New documentation is available at:
>> http://q4md-forcefieldtools.org/REDServer-Development/Documentation/
>> Latest news:
>> http://q4md-forcefieldtools.org/REDServer-Development/news.php
>> Frequently asked questions:
>> http://q4md-forcefieldtools.org/REDServer-Development/faq.php
>> A new tutorial is now available:
>> http://q4md-forcefieldtools.org/Tutorial/
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
>>
>> Users of the R.E.D. III.x tools and of R.E.D. Server (interface of the
>> Ante_RED 2.0 and R.E.D. IV program) are strongly encouraged to switch
>> to R.E.D. Server Development/PyRED.
>>
>> Funding of this project is provided by the Conseil Regional de
>> Picardie and the European Regional Development Fund.
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Received on Tue May 06 2014 - 00:00:03 PDT
