Dear Francois,
thank you for your complex answer and good news
regarding release of the standalone version of
PyRED tool.
Just please do not postpone this release too much
only because the absence of manual because for me (and
perhaps also for many others) your perfect tutorials and eventually,
some examples of input files attached as the part of the program
distribution,
might be also enough.
In case of standalone "RED-III.52-Tools" there was also no manual just
Short HowTo describing mostly attached examples so the related tutorial +
that examples
distributed with this tool was enough for me to learn how to use it.
Meantime I think you may eventually consider to release standalone version
of "R.E.D. IV" tool set.
From your pages and related tutorial:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
seems to me that is highly compatible with "RED-III.52-Tools" so
should not be problem to switch to this "RED-III.52-Tools" successor.
To be frank I am satisfied with "RED-III.52-Tools" but in
"R.E.D. IV" if I remember well there is more extended/automated
atom equvalencing and also the mandatory condition of the same
order of atoms in p2n files corresponding to two different (two
subsequent) extended residues
when inter charge equvalencing is required (INTER-MEQA) is a bit
"uncomfortable" and as far as I remember this condition was removed in
"R.E.D. IV" and perhaps there are also some other improvements
comparing to version III.
Anyway thank you and whole your team for this nice and very very useful
tool
and for its continuous development !
Best wishes,
Marek
Dne Tue, 06 May 2014 08:22:33 +0200 FyD <fyd.q4md-forcefieldtools.org>
napsal/-a:
> 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 - 15:30:03 PDT
