[gmx-users] PROBLEM IN COORDINATES

[neelam wafa]

thanks. problem resolved.

On 21 Feb 2018 08:13, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>