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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>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>
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Received on Thu May 10 2012 - 06:00:03 PDT
