Hi Mohamed,
Sorry about that. You can check the “Gaussian 09 fix” term in this webpage: http://ambermd.org/bugfix_lists_old/bugfixesat.html <http://ambermd.org/bugfix_lists_old/bugfixesat.html>.
Hope it helps,
Pengfei
> On Nov 21, 2019, at 8:50 AM, Mohamed M. Aboelnga <mohamedm.aboelnga.mail.concordia.ca> wrote:
>
> Thanks Pengfei but the provided link for the bug fix is not working! Same thing for the one given in the amber tutorial webpage. So please help in giving any alternatives to fix this bug!
>
> Sincerely,
> Mohamed M. Aboelnga, PhD
> Postdoctoral Fellow
> Centre for Research in Molecular Modeling (CERMM)
> Concordia University, Montreal, Quebec, CANADA
>
> From: Pengfei Li <ambermailpengfei.gmail.com <mailto:ambermailpengfei.gmail.com>>
> Sent: November 20, 2019 8:29 PM
> To: AMBER Mailing List <amber.ambermd.org <mailto:amber.ambermd.org>>
> Subject: Re: [AMBER] Error parameterizing a heme using MCPB
>
> Hi Mohamed,
>
> It is about the version of Gaussian you used.
>
> As noted in the webpage: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm><http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm>> that
> “There is a bug in Gaussian09 rev B.01 when doing the Merz-Kollman population analysis. Please following the "Gaussian 09 fix" section in the Bug Fix Webpage <http://ambermd.org/bugfixesat.html <http://ambermd.org/bugfixesat.html>> to solve the problem."
>
> Hope it helps,
> Pengfei
>
> > On Nov 19, 2019, at 12:20 PM, Mohamed M. Aboelnga <mohamedm.aboelnga.mail.concordia.ca> wrote:
> >
> > Hello Amber users,
> >
> > I am trying to parametrize a Heme group using MCPB.py and I have obtained this error in step 3 of the parametrization procedures. It will be appreciated if anyone could help me addressing this issue. Thanks
> >
> > *======================RESP Charge fitting=======================*
> > * *
> > ******************************************************************
> > ***Generating the 1st stage resp charge fitting input file...
> > ***Generating the 2nd stage resp charge fitting input file...
> > ***Doing the RESP charge fiting...
> > Traceback (most recent call last):
> > File "/cvmfs/restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/cuda/MCPB.py", line 684, in <module>
> > premol2fs, mcresname, 1, chgfix_resids, g0x, lgchg)
> > File "/cvmfs/restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/cuda/python3.6/site-packages/pymsmt/mcpb/resp_fitting.py", line 441, in resp_fitting
> > get_esp_from_gau(mklogf, espf)
> > File "/cvmfs/restricted.computecanada.ca/easybuild/software/2017/avx2/MPI/gcc5.4/cuda/python3.6/site-packages/pymsmt/mol/gauio.py", line 694, in get_esp_from_gau
> > raise pymsmtError("The length of coordinates and ESP charges are different!")
> > pymsmt.exp.pymsmtError: The length of coordinates and ESP charges are different!
> >
> >
> >
> > Sincerely,
> > Mohamed M. Aboelnga, PhD
> > Postdoctoral Fellow
> > Centre for Research in Molecular Modeling (CERMM)
> > Concordia University, Montreal, Quebec, CANADA
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
>
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Received on Mon Nov 25 2019 - 18:30:01 PST
