Kamali,
> Thank you for the confirmation. I just submitted jobs to Ante_RED, and
> everything seems to be working correctly. No problems were caused; I was
> only worried that I may have done something to hurt the server :)
I forgot: the problem you encountered is reported in the FAQ:
http://q4md-forcefieldtools.org/REDS/faq.php#16
If you could "hurt the server" as a client - this would mean the code
would have a big problem... BTW recently we have corrected a series of
bugs/limitations making the communications within R.E.D. Server far
more efficient; however when the network, the electricity power or the
file system is down - it does not work ;-)
regards, Francois
> On Sat, Jul 20, 2013 at 6:14 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Kamali,
>>
>> > It turns out that the standard RESP fitting method using the HF/6-31G*
>> data
>> > set may work for me and my collaborator after all, so we are trying all
>> > different methods (antechamber using different basis sets and solvents
>> with
>> > the HF level of theory, as well as multiple options/conformations in the
>> > RED server) to see how the free energy calculations differ between the
>> > methods. I've been using the RED server all day, but have just now had
>> > trouble generating P2N files. I got a message that some sort of
>> maintenance
>> > was going on, and since then the submission screen that I've gotten after
>> > inputting my PDB files has told me that my file uploads have failed. I've
>> > attached an image of this screen. Is there maintenance going on, or is
>> > there something else wrong?
>>
>> Yes - we got a file system problem sometime yesterday in R.E.D. Server...
>> All should work correctly by now; contact me again if there is a problem.
>> Sorry for the trouble this problem caused...
>>
>> regards, Francois
>>
>>
>>
>> > On Sat, Jul 13, 2013 at 2:14 PM, Kamali Sripathi <ksripath.umich.edu>
>> wrote:
>> >
>> >> Dear Francois,
>> >>
>> >> Thank you very much for your detailed reply. I'm attached to antechamber
>> >> because this protocol is what my collaborators have used successfully to
>> >> generate libraries. Since you've told me that I can modify the RED III x
>> >> source code and we have also narrowed down our search in terms of basis
>> >> set/theory level combinations, I think I will also try RED IIIx as well.
>> >>
>> >> Thank you so much again and have a great weekend,
>> >>
>> >> Kamali
>> >>
>> >>
>> >> On Wed, Jul 10, 2013 at 4:16 AM, FyD <fyd.q4md-forcefieldtools.org>
>> wrote:
>> >>
>> >>> Dear Kamali,
>> >>>
>> >>> IOp(6/33=2) corresponds to the default algo. of the Kollman's group.
>> >>> iop(6/33=2,6/41=10,6/42=17) does not correspond to the default algo...
>> >>> -> I think you should read to understand what these IOP means.
>> >>> http://www.gaussian.com/g_tech/g_ur/k_iop.htm
>> >>> http://www.gaussian.com/g_tech/g_iops/ov6.htm
>> >>> IOp(6/33=2) is not documented; it pnly means 'print the MEP'...
>> >>>
>> >>> Reliable calculations with Antechamber?
>> >>> Do not ask me - I do not use/support Antechamber.
>> >>>
>> >>> You might also be interested in reading the R.E.D. article:
>> >>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
>> >>> Problems (orientation & conformation, algo in MEP computation,
>> >>> chemical equivalencing and charge fitting, etc...) related to MEP
>> >>> computation are described; I hope this describe why R.E.D. was
>> >>> developed...
>> >>>
>> >>> regards, Francois
>> >>>
>> >>>
>> >>> > I've decided to just use the Antechamber method for now, because I'm
>> >>> more
>> >>> > familiar with it. Initially, what I had done is submit output from
>> >>> Ante_RED
>> >>> > to Gaussian. I only had a Link 0 header like this:
>> >>> >
>> >>> > *%Mem=4096MB*
>> >>> > *%NProc=8*
>> >>> > *
>> >>> > *
>> >>> > *#P HF/6-31G* SCF=(Conver=6) NoSymm Test*
>> >>> > * Pop=mk IOp(6/33=2) GFInput GFPrint*
>> >>> > *
>> >>> > *
>> >>> > *MEP - Input generated by R.E.D.-IV MOLECULE*
>> >>> >
>> >>> > while changing the basis set and level of theory. Typically, for
>> >>> > antechamber, my input for the Gaussian has Link0 and Link1 before and
>> >>> after
>> >>> > the molecular structures:
>> >>> >
>> >>> > *%NProc=8*
>> >>> > *%mem=4096MB*
>> >>> > *%chk=sa_charged_gauss101.chk*
>> >>> > *#p opt freq HF/6-31G* formcheck*
>> >>> > *
>> >>> > *
>> >>> > *Title Card Required*
>> >>> > *
>> >>> > *
>> >>> > *--- molecular structure ---*
>> >>> > *
>> >>> > *
>> >>> > *--Link1--*
>> >>> > *%chk=sa_charged_gauss101.chk*
>> >>> > *%mem=4096MB*
>> >>> > *%NProc=8*
>> >>> > *#p HF/6-31G* geom=allcheck guess=read pop=mk
>> >>> iop(6/33=2,6/41=10,6/42=17)*
>> >>> >
>> >>> > Could I submit the first through antechamber and still have reliable
>> >>> > calculations? I know that the grid information is missing in the
>> first
>> >>> > Link0 section I sent you.
>> >>>
>> >>>
>> >>> > On Sun, Jul 7, 2013 at 12:03 PM, FyD <fyd.q4md-forcefieldtools.org>
>> >>> wrote:
>> >>> >
>> >>> >> Dear Kamali,
>> >>> >>
>> >>> >> > Thank you so much for your detailed reply. I have one follow-up
>> >>> question
>> >>> >> > for you: Do you know if it is possible to use Antechamber to
>> generate
>> >>> >> RESP
>> >>> >> > charges using a level of theory other than HF/6-31G*?
>> >>> >>
>> >>> >> I would answer try and see ;-) Antechamber (and R.E.D.) just take
>> the
>> >>> >> MEP computed by QM and perform charge fitting whatever is the QM
>> >>> >> theory level...
>> >>> >>
>> >>> >> You could also download R.E.D. III.x; modify the source code so that
>> >>> >> the 'RESP-A1' charge model use the QM theory level of your choice...
>> >>> >>
>> >>> >> regards Francois
>> >>> >>
>> >>> >> PS If you need it we can modify the source of R.E.D. for you...
>> >>> >>
>> >>> >>
>> >>> >> > On Thu, Jul 4, 2013 at 10:51 AM, FyD <
>> fyd.q4md-forcefieldtools.org>
>> >>> >> wrote:
>> >>> >> >
>> >>> >> >> Dear Kamali,
>> >>> >> >>
>> >>> >> >> > I actually do have another question. I would like to generate
>> >>> charges
>> >>> >> >> using
>> >>> >> >> > a basis set besides HF/6-31G* and AM1-BCC, and I was wondering
>> if
>> >>> (a)
>> >>> >> the
>> >>> >> >> > RED Server has or will have such a potential, and (b) if you
>> have
>> >>> any
>> >>> >> >> > suggestions about generating charges with other, non-standard
>> >>> basis
>> >>> >> sets.
>> >>> >> >>
>> >>> >> >> The use of HF/6-31G* is related to implicit polarization
>> requested
>> >>> in
>> >>> >> >> the additive Amber force field model. See
>> >>> >> >> http://ambermd.org/doc6/html/AMBER-sh-19.4.html#sh-19.4
>> >>> >> >> Be aware of what you do when using MP2 or DFT methods. For
>> instance
>> >>> >> >> MP2/aug-cc-pTVZ is used in the non-additive/polarizable FF model.
>> >>> >> >>
>> >>> >> >> Concerning AM1-BCC, the later approach is supposed to be an
>> >>> >> >> 'approximation/simplification' of the RESP approach. Considering
>> >>> that
>> >>> >> >> HF/6-31G* cost nothing (from a cpu point of view) our days I do
>> not
>> >>> >> >> understand why one would need an 'approximation' of the RESP
>> >>> method...
>> >>> >> >> and obviously approximation/simplification has nothing to do with
>> >>> >> >> breaking chemical equivalencing (just my personal opinion)...
>> >>> >> >>
>> >>> >> >> R.E.D. Server charge models are described at:
>> >>> >> >> http://q4md-forcefieldtools.org/REDS/popup/popkeyword.php
>> >>> >> >> R.E.D. Server Development charge models are described at:
>> >>> >> >>
>> >>> http://q4md-forcefieldtools.org/REDS-Development/popup/popkeyword.php
>> >>> >> >>
>> >>> >> >> regards, Francois
>>
>>
>>
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>
F.-Y. Dupradeau
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Received on Sat Jul 20 2013 - 10:00:03 PDT
