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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> >>>
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Received on Mon May 14 2012 - 17:30:04 PDT
