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 15 2012 - 11:00:03 PDT
