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 Tue May 29 2012 - 23:00:03 PDT
