[gmx-users] [gmx-user] coordinates mismatch error

[Quin K]

Thanks you!!
I had forgotten to include the ligand atoms in the .gro file.
I was able to correct the error!
*Wishing you are Happy 2020~!*
Thanks for all the help!!

On Tue, Dec 31, 2019 at 9:15 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/31/19 9:43 AM, Quin K wrote:
> > Could it be due to protein-ligand complex being at the edge of the box?
> >
> https://drive.google.com/file/d/187fPACfq1QybNJxkyJKB8faUPOBRFccK/view?usp=sharing
>
> Your link requires permission to view, but in any case, no, this has
> nothing to do with the error.
>
> The solution to this error is always the same - proper bookkeeping. You
> have a difference of 69 atoms that are in the coordinates but not the
> topology. How many atoms are in your ligand? Do you have the right
> number of water molecules specified?
>
> -Justin
>
> >
> >
> > On Tue, Dec 31, 2019 at 8:06 PM Quin K <profiles.ke at gmail.com> wrote:
> >
> >> Hi
> >>
> >> I continue to get following error during complex MD
> >>
> >>
> >>
> >> *number of coordinates in coordinate file (solv.gro, 50670)does not
> match
> >> topology (topol.top, 50701)*
> >> I don't understand why there's a mismatch.
> >> I followed the instructions in mdtutorials.com for Gromacs
> ligand-protien
> >> complex.
> >>
> >> How can I rectify this?
> >>
> >> Regards
> >>
> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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>
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> http://www.thelemkullab.com
>
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