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 - 12:00:14 PDT
