OK, perfect !
As I am used to use version III where is necessary
to set most of chem. equiv. by hand I have no problem
just to check if RED-IV simply did a good automated job :))
Thanks in advance for RED-IV scripts !
Best wishes,
Marek
Dne Wed, 07 May 2014 20:38:09 +0200 FyD <fyd.q4md-forcefieldtools.org>
napsal/-a:
> Marek,
>
>> 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 :)) ).
>
> I can indeed find some free nanoseconds ;-) to send to your personal
> address RED IV & Ante_RED 2.0. RED IV is quite stable; this is just
> that one get lots in the source code when one wants to add new
> features (this is a script; not a program)...
>
>> 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 ?
>
> CH3-CH2-CH2-CH2-CH2-CH2-CH2-OH
> Ante_R.E.D. 2.0 get lost between these CH2 groups
> & Ante_R.E.D. 1.x works well (but this is by luck)
>
> CH3
> CH3-C-CH2-CH-CH2-CH2-CH2-CH3
> CH3 OH
> - Ante_R.E.D. 1.x does not do the job (but this is known)
> - Ante_R.E.D. 2.0 does the job correctly as it should do
>
> In all the cases one always has to check/modify the P2N file...
>
> PyRED does not need that P2N file and does chem. equiv. correctly so
> far ;-) directly from the PDB file format (whatever atom names there
> are in the file).
>
> regards, Francois
>
>
>
>> 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 - 12:30:04 PDT
