Hello Francois, RED server job is P8184 for the ante-red job and P8185
for the actual geometry optimization and resp fit.
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.
Thank you again.
Best regards
Fabrício
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 - 20:00:03 PDT
