Hi Prasanth,
The warning message speaks for itself:
"pymsmt.exp.pymsmtError: The coordinates number in fchk file are not consistent with the atom number."
Check whether you had modified the Gaussian input files by adding or deleting any atoms from the original files.
Either adding, deleting, or re-numbering the atoms in the Gaussian input files can cause error.
Hope it helps,
Pengfei
> On Feb 4, 2019, at 8:43 AM, Prasanth G, Research Scholar <prasanthghanta.sssihl.edu.in> wrote:
>
> Dear all,
>
> I am interested in working with a nonheme containing iron protein. I was
> following the MCPB.py tutorial for this purpose.
>
> I had carried out the gaussian (g09) to obtain the .frchk file. However in
> the second step while executing the command to carry out seminario method
> to obtain the forcefield parameters..
>
> $ MCPB.py -i 3o8y.in -s 2
>
> I obtained this error -
>
> ******************************************************************
> * *
> *===================Generate the Initial frcmod file=============*
> * *
> ******************************************************************
> Atoms which has changed the atom types: [5877, 5970, 8791, 10751, 10754]
> 363-HID.5877-NE2 : NB --> Y1
> 368-HID.5970-NE2 : NB --> Y2
> 546-HID.8791-NE2 : NB --> Y3
> 669-ILE.10751-O : O2 --> Y4
> 670-FE.10754-FE : LP --> M1
> ==================Using the Seminario method to solve the problem.
> Traceback (most recent call last):
> File "/home/cosmos10/Prasanth/amber16/bin/MCPB.py", line 662, in <module>
> fcfchkf, fclogf, g0x, scalef, bondfc_avg, anglefc_avg)
> File
> "/home/cosmos10/Prasanth/amber16/lib/python2.7/site-packages/pymsmt/mcpb/gene_final_frcmod_file.py",
> line 729, in gene_by_QM_fitting_sem
> crds = get_crds_from_fchk(chkfname, len(atids))
> File
> "/home/cosmos10/Prasanth/amber16/lib/python2.7/site-packages/pymsmt/mol/gauio.py",
> line 398, in get_crds_from_fchk
> raise pymsmtError('The coordinates number in fchk file are not
> consistent '
> pymsmt.exp.pymsmtError: The coordinates number in fchk file are not
> consistent with the atom number.
> ---
> Could someone help me in rectifying this issue..?
> Thanks in advance.
>
> --
> Regards,
> Prasanth.
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Received on Tue Feb 05 2019 - 09:00:02 PST
