Re: [AMBER] MCPB.py & error: coordinates number in fchk file are not consistent with the atom number

From: Pengfei Li <ambermailpengfei.gmail.com>
Date: Fri, 8 Feb 2019 22:03:02 -0500

Dear Prasanth,

The atom names in fchk file (if there are, but I do not think so) do not matter at all, only the Hessian matrix in the fchk file matter, which does not have atom name information at all.

There are only four steps of MCPB.py modeling, and all of them are essential. Skipping a step will not work.

If your final force constant calculation has the same amount of atoms as the small model PDB file, and only the sequence is different. You can use the local minima structure you got, and manually re-sequence the structure according to the atom sequence in the small model PDB file, and then carry out a new force constant calculation. Finally the generated fchk file for the new calculations can be used.

If your final force constant calculation does not have the same amount of atoms as the small model PDB file, I would suggest you to redo completely. But you can refer the local minima structure you already got (again, need to delete or add atoms to match exactly the atom number and sequence in the small model PDB file) for doing minimization and force constant calculation. This is because there will be a Hessian matrix generated in the force constant calculation, and sequence of the matrix is completely depend on the atom sequence in the calculations. Any adding or deleting atoms will shift the matrix sequence (and MCPB.py can not recover it to the ÔÇťoriginal" sequence by itself).

Moreover, I would not suggest you to change the generated PDB files and fingerprint files, in order to match the atom sequence in the quantum calculations, because that may cause more problems. Just keep the small model PDB file as it was generated.

The above principles also apply for the Merz-Kollman charge calculations for the large model.

Hope it helps,
Pengfei

> On Feb 6, 2019, at 5:06 AM, Prasanth G, Research Scholar <prasanthghanta.sssihl.edu.in> wrote:
>
> Dear Pengfei,
>
> Unfortunately, we did modify the double bonds and in that process, the
> hydrogens got deleted and we had to manually add the same (in Gaussian).
> Is there any way, we can still use the output files.
>
> option 1: can we substitute the names of the atoms from the input file into
> the fchk file? If yes, how can it be done?
> option 2: would it work if i carried out the steps from start till the
> creation of fchk file and skip the last step (with large_mk.com)?
> option 3: redo completely..!
>
> It has taken about 15 days to get these results, I am just hoping that
> there is a way, in which it can be fixed.
>
> Thank you,
> Reagards,
> Prasanth.
>
>
> In response to Pengfei's response
> ---
> 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.
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> AMBER.ambermd.org
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Received on Fri Feb 08 2019 - 19:30:02 PST
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