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 Sat Jul 20 2013 - 03:30:02 PDT
