Dear Francois,
I have one question for clarification:
I'm trying to make a library for a central protonated adenosine, and to
compare charge methods I've been using both option 2 and option 3 with
single and multiple conformations in the RED Server. I have not been using
any intra- or inter-molecular charge constraints; I think this is all
right, but I just wanted to double-check.
For option 2, I'm uploading central fragments of the nucleotide (with a 5'
phoshpate and 3'O), so I think no inter-molecular charge constraints need
to be specified, is that right? And I have not specified any
intra-molecular constraints but have noticed, for example, that adenine's
exocyclic amine hydrogens and the nonbridging oxygens have the same
charges.
Similarly, I shouldn't need to specify any intra- or inter-molecular charge
constraints because I submit the nucleoside and Option 3 supplies the
dimethylphosphate. I was assuming that Option 3 would also take care of the
inter-molecular charge constraints for the dimethyl phosphate.
Thank you so much, and have a great day and weekend,
Kamali
On Sun, Jul 21, 2013 at 11:01 PM, Kamali Sripathi <ksripath.umich.edu>wrote:
> Dear Francois,
>
> Thanks a lot for the information and the answers. I know that a user
> bringing down a server is very unlikely, but I often worry about the slight
> possibility. :)
>
> Thanks so much again, and have a great night,
>
> Kamali
>
>
> On Sat, Jul 20, 2013 at 12:54 PM, FyD <fyd.q4md-forcefieldtools.org>wrote:
>
>> 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
>> >>
>> >>
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>>
>>
>>
>> F.-Y. Dupradeau
>> ---
>> http://q4md-forcefieldtools.org/FyD/
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
>
--
Kamali Sripathi
PhD Candidate, Medicinal Chemistry
Walter Laboratory
930 North University
Ann Arbor, MI, 48109
ksripath.umich.edu
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Received on Thu Jul 25 2013 - 09:00:02 PDT
