[gmx-users] PROBLEM IN COORDINATES

[Justin Lemkul]

On 2/20/18 9:50 PM, neelam wafa wrote:
> Dear gmx users
>
> I am still stuck at this point.
> error obtained is this
> Fatal error:
> number of coordinates in coordinate file (solv.gro, 32803)
>               does not match topology (topol.top, 32818)
> There is a difference of 15. I think its not considering the ligand as 15
> is i think for ligand. the ligand. the entries of ligand in gro file are
> these.
> 15
>      1JZ4  C4       1   2.946  -2.601   0.141
>      1JZ4  C14      2   3.009  -2.568   0.005
>      1JZ4  C13      3   2.965  -2.664  -0.107
>      1JZ4  C12      4   2.834  -2.642  -0.154
>      1JZ4  C11      5   2.734  -2.734  -0.116
>      1JZ4  H11      6   2.753  -2.810  -0.040
>      1JZ4  C7       7   2.606  -2.727  -0.176
>      1JZ4  H7       8   2.529  -2.798  -0.147
>      1JZ4  C8       9   2.578  -2.628  -0.273
>      1JZ4  H8      10   2.479  -2.624  -0.319
>      1JZ4  C9      11   2.677  -2.536  -0.311
>      1JZ4  H9      12   2.655  -2.460  -0.387
>      1JZ4  C10     13   2.804  -2.543  -0.251
>      1JZ4  OAB     14   2.900  -2.451  -0.285
>      1JZ4  HAB     15   2.863  -2.389  -0.354
>     0.68000   0.68000   0.68000
>
> Help me out please.

Looks like you probably didn't copy the ligand coordinates into the 
topology. The topology thinks it's there and the coordinates say it's 
not. The solution to this error is always the same: proper bookkeeping.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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