Dear Francois,
thank you again !
I am already registered ( several times :)) ) so when you
find some free nanosecond please send me the RED-IV scripts
( the least buggy subversion please :)) ).
BTW, what exactly do you mean by the :
"for chains with 4 or 5 repetitive groups the chem. equiv. algo
in Ante_RED 2.0 is broken;"
Can you eventually show some concrete example of such situation ?
Thank you,
Best wishes,
Marek
Dne Wed, 07 May 2014 17:05:26 +0200 FyD <fyd.q4md-forcefieldtools.org>
napsal/-a:
> 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 - 10:00:04 PDT
