[gmx-users] PROBLEM IN COORDINATES

neelam wafa neelam.wafa at gmail.com
Wed Feb 21 03:50:10 CET 2018


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.

Regards

On Sun, Feb 18, 2018 at 6:45 PM, Alex <nedomacho at gmail.com> wrote:

> Hi,
>
> The error is informative. Check the number of entries in the gro file and
> compare it with the [ atoms ] section in your topology, together with
> anything that's added under [ system ]. The total numbers need to match.
>
> Alex
>
>
>
> On 2/18/2018 11:34 AM, neelam wafa wrote:
>
>> Dear gmx users,
>>
>> I am doing the tutorial of protein ligand simmulation given at
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>> -tutorials/com.
>> when I give following command, I get an error.
>>
>> gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>>
>> the error says the number of coordinates in the sol.gro file and
>> topol.top file does not match. How to fix it.
>>
>> Help me out please.
>>
>> Thanks in advance.
>>
>> Regards
>>
>
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