Dear Francois,
Thank you very much for your detailed response, and I'm sorry for not
including my job number. I felt my question was more general, and so didn't
think the job number was necessary. I've also read over the links you sent
me, but I just wanted to make sure.
Thank you so much again, and have a great weekend,
Kamali
On Fri, Jul 26, 2013 at 4:36 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Kamali,
>
> See http://q4md-forcefieldtools.org/REDS/faq.php#5
> When describing the problem you encountered with R.E.D. Server, please
> also provide the 'PXXXX' R.E.D. Server job name in the body of your
> email so that we can more easily assist you.
>
> > 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.
>
> I guess option 2 & option 3 corresponds to:
> http://q4md-forcefieldtools.org/Tutorial/images/Nuc-frag.jpg
> i.e.
> Use R.E.D. IV
> Use R.E.D. IV for auto... nucleotide fragments
> right?
>
> > 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.
>
> For option 2 (if I well understood); see :
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#26
> you need to upload whole molecules _and not_ molecular fragments!
> -> R.E.D. generates mol. fragments _from_ the whole molecules
> uploaded by the user based on the constraints defined in the P2N
> files. See once again:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#26
> First P2N file for dimethylphosphate (DMP):
> http://q4md-forcefieldtools.org/Tutorial/P2N/All-frag-Nuc/Mol_red1.p2n
> -> constraints (between the 2 methyl groups of DMP and the HO5 & HO3
> groups of the nucleoside) are defined in this P2N file:
> REMARK INTER-MCC 0.0 | 1 2 | 10 11 12 13 | 1 2
> REMARK INTER-MCC 0.0 | 1 2 | 1 2 3 4 | 3 4
> Second P2N file:
> http://q4md-forcefieldtools.org/Tutorial/P2N/All-frag-Nuc/Mol_red2.p2n
> i.e. the nucleoSIDE.
>
> > 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.
>
> In option 3 (if I well understood again); see :
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#27
>
> you just provide the P2N file for your nucleoside; no need to add the
> constraints - they are automatically determined...
>
> regards, Francois
>
>
>
> > 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
> >>> >>
>
>
>
>
>
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Received on Fri Jul 26 2013 - 05:00:03 PDT
