Dear Francois,
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 :)
Thanks so much again, and have a great weekend,
Kamali
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
Received on Sat Jul 20 2013 - 06:00:03 PDT
