Fabrício,
> Thank you for the tips. I'll rename the residues so that I end up
> working with one single residue name. As for the intra-mcc, apart fro
> the NMe and MeCO cap charges, would it be a wise distribution to set
> the constraints also for each residue in addition to the resulting
> charge of the entire complex?
well, if you want to insert your complex back into a protein, you need
to generate a fragment for your complex, and using intra-molecular
charge constraints on the ACE and NME capping groups is _one_ way to
do it...
See
http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract
> I found out that I am still using Gaussian Rev B.01. I've seen that
> gaussian09 Rev. C.01 has been changed to deal explicitly with
> iop(6/50=1) for charge generation for RESP. I've checked the espgen
> command with ethylamine and the result was the same (even after
> applying fixreadinesp.sh). Perhaps this problem was fixed with the
> latest revision of gaussian.
Yes, this is fixed in the Gaussian 2009 C.01 version...
If you look at R.E.D. Server the Gaussian 2009 A.01 version was
interfaced and now C.01 is interfaced, but the version B.01 was/is
never interfaced ;-)
regards, Francois
> 2012/5/30 FyD <fyd.q4md-forcefieldtools.org>:
>> Dear Fabrício
>>
>>> RED server job is P8184 for the ante-red job and P8185
>>> for the actual geometry optimization and resp fit.
>>
>> I checked your jobs & they look ok to me. Several remarks:
>> - Generating a single residue for your entire complex might be more
>> simple when using it in LEaP (and obviously two atoms belonging to a
>> given residue cannot share the same name).
>> - You decided to add a HO(-) instead of a water molecule...
>> - You need to define several (6_?) INTRA-MCC to generate the
>> corresponding fragment
>> see : http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
>> but in your case this is for all the dipeptide ligands...
>> - You need to wonder if the theory level used in geometry
>> optimization/MEP computation is correct. You might need to switch to
>> R.E.D. Server Dev. to use other theory levels...
>>
>>> I'll try to do the way you suggested. But I still would like to know
>>> why my espgen version does not work with my gaussian09 files.
>>
>> this is not yet solved? (I did not read all the emails about "MCPB
>> espgen error")...
>> - is it a bug?
>> - did you try using a small organic molecule? does it work?
>>
>> regards, Francois
>>
>>
>>> 2012/5/19 FyD <fyd.q4md-forcefieldtools.org>:
>>>> Dear Fabrício,
>>>>
>>>>> I've tried inputting the active site I am trying to parameterize (with
>>>>> the residues linked to Zn metal) into R.E.D. server. The calculation
>>>>> worked out ok, but the problem is that in order to generate the
>>>>> necessary p2n file I have used the server also, and the p2n file comes
>>>>> out with a different order of atoms than that of the original pdb one
>>>>> (even though I marked on the server's options to keep current order).
>>>>
>>>> if you request to keep the input order; this order should be conserved...
>>>> or there is a bug... if you provide us the PXXXX R.E.D. Server job; I
>>>> should be able to look at this job...
>>>>
>>>> the best approach might be to build a single residue in the PDB input
>>>> file; then generate the P2N file.
>>>>
>>>>> Is that going to be a problem?
>>>>
>>>> more generally letting R.E.D. Server/Ante_R.E.D. 2.0 to choose the
>>>> atom order is not a problem if you use R.E.D. Server/R.E.D. IV in its
>>>> "mode 1" i.e. if you let R.E.D. Server/R.E.D. IV to perform the
>>>> geometry optimization step.
>>>> See http://q4md-forcefieldtools.org/REDS/popup/popredmodes.php
>>>>
>>>>> Also, using the R.E.D. server only got
>>>>> me a mol2 file and loads of resp fitting output files. The RESP
>>>>> procedure given on the MTKpp manual results in amber prep, frcmod and
>>>>> FF modification files. What do I do to get there with R.E.D?
>>>>
>>>> once you got the mol2 file generated by R.E.D., atom types (and new
>>>> atom types) have to be added using a LEaP script (you can find many
>>>> examples in R.E.DD.B. projects; see the script1.ff)
>>>> then, you request LEaP to save the prmtop/prmcrd files and LEaP will
>>>> list the missing FF parameters. Here, we create by hand the frcmod
>>>> file in agreement with the new atom types defined in the LEaP script
>>>> and with the QM fit used to develop the missing FF parameters...
>>>>
>>>> You can find an example of bio-inorganic complex in R.E.DD.B. .
>>>> http://q4md-forcefieldtools.org/REDDB/projects/F-88/
>>>> http://q4md-forcefieldtools.org/REDDB/projects/F-88/script1.ff
>>>> vs
>>>> http://q4md-forcefieldtools.org/REDDB/projects/F-89/
>>>> http://q4md-forcefieldtools.org/REDDB/projects/F-89/script1.ff
>>>>
>>>> here you will find ESP vs RESP charges + two types of topology by
>>>> project; i.e. with and without atom connectivities between the metal
>>>> center and the ligands...
>>>>
>>>> regards, Francois
>>>>
>>>>
>>>>> 2012/5/15 Fabrício Bracht <bracht.iq.ufrj.br>:
>>>>>> Hello Robin. Thank you for the reply. What do you think is best for me
>>>>>> to do? Wait for the bugfix or get in touch with Junmei?
>>>>>> And how would I get in touch with him?
>>>>>> Thank you
>>>>>> Fabrício
>>>>>>
>>>>>> 2012/5/14 Robin Betz <rbetz.ucsd.edu>:
>>>>>>> Hi Fabricio,
>>>>>>>
>>>>>>> It looks like there have been updates to espgen in the development tree
>>>>>>> since the release of AmberTools12, as "vanilla" espgen does output the
>>>>>>> error you're seeing when faced with Gaussian 09 input files,
>>>>>>> and support
>>>>>>> for these has since been added. You may want to ask the
>>>>>>> developer, Junmei
>>>>>>> Wang, for a copy of the newer version, or wait for it to be
>>>>>>> released in a
>>>>>>> bugfix soon.
>>>>>>>
>>>>>>> Regards,
>>>>>>> Robin
>>>>>>>
>>>>>>> On Thu, May 10, 2012 at 5:40 AM, Fabrício Bracht
>>>>>>> <bracht.iq.ufrj.br> wrote:
>>>>>>>
>>>>>>>> As I said in the last email, I ran again the calculation using # opt
>>>>>>>> b3lyp/6-31g(d) geom=connectivity integral=grid=ultrafine iop(6/50=1)
>>>>>>>> pop=(mk,readradii) scf=xqc
>>>>>>>>
>>>>>>>> The result is the same. Once the script runs espgen the error message
>>>>>>>> comes out the same way.
>>>>>>>> By the way, did you fing the error message I pointed out on line 430
>>>>>>>> of the espgen.c?
>>>>>>>> Thank you
>>>>>>>> Fabrício
>>>>>>>>
>>>>>>>> 2012/5/9 Fabrício Bracht <bracht.iq.ufrj.br>:
>>>>>>>> > Hi Robin. I found the exact line on espgen.c.
>>>>>>>> > "espgen cannot deal with Gaussian 09 log file, please generate
>>>>>>>> > Gaussian 09 ESP file using iop(6/50=1) and rerun espgen" on line 430
>>>>>>>> > of the espgen.c file.
>>>>>>>> > I am using AmberTools12. Here is the
>>>>>>>> > # b3lyp/6-31g(d) geom=connectivity integral=grid=ultrafine
>>>>>>>> iop(6/50=1)
>>>>>>>> > pop=(mk,readradii) scf=xqc
>>>>>>>> > I am running the calculation again with the "opt" added
>>>>>>>> before b3lyp.
>>>>>>>> > Maybe that's the problem. Once the calculation is finished I'll let
>>>>>>>> > you know.
>>>>>>>> > Fabrício
>>>>>>>> >
>>>>>>>> > 2012/5/8 Robin Betz <rbetz.ucsd.edu>:
>>>>>>>> >> Hi Fabricio,
>>>>>>>> >>
>>>>>>>> >> The code for espgen is fairly simple if you know C. You can look
>>>>>>>> >> through it in $AMBERHOME/AmberTools/src/antechamber/espgen.c and
>>>>>>>> >> search for the line with your error to see what the code is getting
>>>>>>>> >> stuck on.
>>>>>>>> >> Are you running AmberTools12? I can't find your error
>>>>>>>> message in the
>>>>>>>> >> code for the latest version of espgen.
>>>>>>>> >> What is your instruction line for Gaussian in your ESP .com file?
>>>>>>>> >> Espgen looks for output obtained from using the opt keyword
>>>>>>>> instead of
>>>>>>>> >> just a single point calculation.
>>>>>>>> >>
>>>>>>>> >> Regards,
>>>>>>>> >> Robin Betz
>>>>>>>> >> UC San Diego
>>>>>>>> >>
>>>>>>>> >> On Tue, May 8, 2012 at 4:12 AM, Fabrício Bracht <bracht.iq.ufrj.br>
>>>>>>>> wrote:
>>>>>>>> >>
>>>>>>>> >>> Hi. I've narrowed down the problem to the espgen routine. It seems
>>>>>>>> >>> that espgen cannot handle gaussian09 output files. When I
>>>>>>>> run espgen
>>>>>>>> >>> -i input_mk.log -o output_mk.esp the error comes out the
>>>>>>>> same. "espgen
>>>>>>>> >>> cannot deal with Gaussian 09 log file, please generate
>>>>>>>> Gaussian 09 ESP
>>>>>>>> >>> file using iop(6/50=1) and rerun espgen".
>>>>>>>> >>> What does exactly espgen does? If the case is justo to
>>>>>>>> remove the esp
>>>>>>>> >>> information from the output file, maybe I could do it by
>>>>>>>> hand or using
>>>>>>>> >>> a script.
>>>>>>>> >>> Thank you
>>>>>>>> >>> Fabrício
>>>>>>>> >>>
>>>>>>>> >>> 2012/5/7 FyD <fyd.q4md-forcefieldtools.org>:
>>>>>>>> >>> > Dear Fabrício,
>>>>>>>> >>> >
>>>>>>>> >>> > You might try R.E.D. Server as well...
>>>>>>>> >>> >
>>>>>>>> >>> > regards, Francois
>>>>>>>> >>> >
>>>>>>>> >>> >
>>>>>>>> >>> >> Hi there. I've sent this message almost a week ago but
>>>>>>>> didn't get
>>>>>>>> any
>>>>>>>> >>> >> reply. I think my email server is not working properly and
>>>>>>>> the email
>>>>>>>> >>> >> was actuallly never sent. Therefore I am sending the
>>>>>>>> message again
>>>>>>>> in
>>>>>>>> >>> >> hope that it will be delivered correctly. Thank you
>>>>>>>> and apologies
>>>>>>>> for
>>>>>>>> >>> >> any inconvenience.
>>>>>>>> >>> >>
>>>>>>>> >>> >> Message below:
>>>>>>>> >>> >>
>>>>>>>> >>> >> I've been trying to follow the tutorial in MTKpp.pdf
>>>>>>>> in order to
>>>>>>>> >>> >> create the parameters for my zinc active site. I've
>>>>>>>> been able to
>>>>>>>> >>> >> modify the scripts all right until I got to the part where the
>>>>>>>> >>> >> tutorial tells you about the RESP fit (page 92, section
>>>>>>>> 15-10-11).
>>>>>>>> One
>>>>>>>> >>> >> thing I didn't understand is that the tutorial says that
>>>>>>>> there are 4
>>>>>>>> >>> >> files relating to different charge models, but the
>>>>>>>> example is only
>>>>>>>> >>> >> given for:
>>>>>>>> >>> >>
>>>>>>>> >>> >> MCPB -i 1AMP_OH_large_mk1.bcl -l 1AMP_OH_large_mk1.bcl.log
>>>>>>>> >>> >> mv 1AMP_OH_large_respAdds 1AMP_OH_large_respAdds1
>>>>>>>> >>> >> sh ./getCharges.sh 1
>>>>>>>> >>> >>
>>>>>>>> >>> >> Does this mean I have to perform this sequence of
>>>>>>>> commands for each
>>>>>>>> of
>>>>>>>> >>> the 4?
>>>>>>>> >>> >>
>>>>>>>> >>> >> Second question is: I get an error when I run "sh
>>>>>>>> ./getCharges.sh
>>>>>>>> >>> >> 1", which is
>>>>>>>> >>> >>
>>>>>>>> >>> >> espgen cannot deal with Gaussian 09 log file, please generate
>>>>>>>> Gaussian
>>>>>>>> >>> >> 09 ESP file using iop(6/50=1) and rerun espgen
>>>>>>>> >>> >>
>>>>>>>> >>> >> Fragment resp charge fitting
>>>>>>>> >>> >> 1AMP_OH_large_mk is the 3 letter residue name
>>>>>>>> >>> >>
>>>>>>>> >>> >> RESP stage 1:
>>>>>>>> >>> >> At line 840 of file resp.F (unit = 10, file =
>>>>>>>> '1AMP_OH_large_mk.esp')
>>>>>>>> >>> >> Fortran runtime error: End of file
>>>>>>>> >>> >> Error: check .out and try again
>>>>>>>> >>> >> mv: cannot stat `1AMP_OH_large_mk.resp2.chg': No such file or
>>>>>>>> directory
>>>>>>>> >>> >>
>>>>>>>> >>> >> I've already verified and my gaussian .com for the large
>>>>>>>> model and
>>>>>>>> it
>>>>>>>> >>> >> had the iop(6/50=1).
>>>>>>>> >>> >> Any help here would be nice.
>>>>>>>> >>> >> Thank you
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Received on Thu May 31 2012 - 13:00:04 PDT
