[gmx-users] Number of cooredinate in topol.top and solv.gro not matching

[Justin A. Lemkul]

On 5/2/12 1:09 PM, Sangita Kachhap wrote:

>>> I have to do MD simulation of ligand bound membrane protein in lipid bilayer.
>>> Thus I am doing tutorialfor Protein - Ligand tutorial:
>>>
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
>>>
>>> I have used following command:
>>>
>>> pdb2gmx -f 3HTB_clean.pdb -o conf.gro -water spc
>>>
>>> editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
>>>
>>> genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
>>>
>>> grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>>>
>>> I am getting stuck at last command. Its showing following error:
>>>
>>> Fatal error:
>>> number of coordinates in coordinate file (solv.gro, 33049)
>>>                does not match topology (topol.top, 33064)
>>> For more information and tips for troubleshooting, please check the GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>>
>>
>> Did you follow the link?  Did you read
>> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>> ?
>>
>>> {But when I calculate number of atom in topol.top and solv.gro it is same}
>>>
>>
>> That's not possible.
>>
>>> When I checked above http: I got that such type of error may be due to cpp
>>> variable is not properly set in the .mdp file.
>>> But When I locate ccp in my system and add it to .mdp file.
>>>
>>> "
>>> ; LINES STARTING WITH ';' ARE COMMENTS
>>> title           = Minimization  ; Title of run
>>> cpp             =/usr/bin/cpp
>>> ; Parameters describing what to do, when to stop and what to save
>>>                 "
>>>
>>> Then also it showing same error.
>>>
>>> Please help me to solve this problem.
>>>
>>> I am using gromacs-4.5.5 and installed with fftw-3.3.1 .
>>>
>>
>> The cpp parameter is ignored for all Gromacs versions as of 4.5.
>>
>> Your problem is that you don't have a ligand in your coordinate file.  Note that
>> you're off by 15 atoms, which is exactly how many are in the ligand described in
>> the tutorial.  Go back and read the instructions closely, as appending the
>> ligand to the protein coordinate file is discussed in detail.
>
>
>
> Thanks for reply
>
> When I am appending ligand from .gro file and generating complex the new .gro
> file newbox.gro do not have ligand.
>
> Command I have used:   editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
>
> I am appending ligand like this at the end of conf.gro
>
>    163ASN   HD21 1689   1.029  -0.671  -0.401
>    163ASN   HD22 1690   0.944  -0.584  -0.525
>    163ASN      C 1691   0.621  -0.740  -0.126
>    163ASN     O1 1692   0.624  -0.616  -0.140
>    163ASN     O2 1693   0.683  -0.703  -0.011
>      1JZ4  C4       1   2.429  -2.412  -0.007
>      1JZ4  C14      2   2.392  -2.470  -0.139
>      1JZ4  C13      3   2.246  -2.441  -0.181
>      1JZ4  C12      4   2.229  -2.519  -0.308
>      1JZ4  C11      5   2.169  -2.646  -0.295
>      1JZ4  H11      6   2.135  -2.683  -0.199
>      1JZ4  C7       7   2.155  -2.721  -0.411
>      1JZ4  H7       8   2.104  -2.817  -0.407
>      1JZ4  C8       9   2.207  -2.675  -0.533
>      1JZ4  H8      10   2.199  -2.738  -0.621
>      1JZ4  C9      11   2.267  -2.551  -0.545
>      1JZ4  H9      12   2.306  -2.516  -0.640
>      1JZ4  C10     13   2.277  -2.473  -0.430
>      1JZ4  OAB     14   2.341  -2.354  -0.434
>      1JZ4  HAB     15   2.369  -2.334  -0.528
>     5.99500   5.19182   9.66100   0.00000   0.00000  -2.99750   0.00000   0.00000
>    0.00000
>

Have you correctly incremented the second line of conf.gro to indicate that more 
atoms have been added?  Without it, editconf will read the wrong number of lines 
and exclude the ligand.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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