Re: [AMBER] Antechamber atom types and all_nuc94.in atom descriptions

From: Kamali Sripathi <ksripath.umich.edu>
Date: Fri, 19 Jul 2013 15:20:44 -0400

Dear Francois,

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?

Thank you so much for your patience,

Kamali


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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>>
>
>
>


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Received on Fri Jul 19 2013 - 12:30:02 PDT
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