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
> >>
> >>
> >>
> >> _______________________________________________
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> >> 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/
>
>
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Received on Sun Jul 21 2013 - 20:30:02 PDT
