Dear Marek,
> 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.
Perfect? ... Well ... many tutorials are missing:
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#NEWTUTO
and many keywords are even not documented; we have more than 80 keywords...
We do our best; every day we add new features;
This morning:
http://q4md-forcefieldtools.org/REDServer-Development/popup/poparchive.php
because users have problems with that archive
This afternoon two systems of geometrical constraints are
implemented for geometry optimization for the different versions of
Gaussian as requested by a user.
> 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.
Yes but all the features were described - shortly described, but described...
this is not the case for PyRED...
> Meantime I think you may eventually consider to release standalone version
> of "R.E.D. IV" tool set.
We cannot spend time on that perl versions anymore; if a user wants to
get RED IV he can just contact us; we will be glad to send that
version; just register to get the RED III.x tools and we will send RED
IV/Ante_RED 2.0...
> 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.
Yes you are right RED III.x & IV are compatible
> 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
Yes but for chains with 4 or 5 repetitive groups the chem. equiv. algo
in Ante_RED 2.0 is broken; that in Antechamber might be slightly
better but breaks also with multiple cycles ;-) No problem with PyRED
so far...
> 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.
if I remember RED IV contains two types of inter-meq i.e. a/b and is
more multiple molecules oriented, but buggy when intermcc/intermeq are
not applied is the 1st P2N file of the whole list...
regards, Francois
> 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 Wed May 07 2014 - 08:30:06 PDT
