[gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093)

[swati rana]

Thanx a lot that helped... but now there is one more issue. I am consulting
the site for each and every error and getting most of the help but these
are few which i am not able to resolve even after referring to the site.

After running the energy minimization step i am facing the following error:

-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/confio.c, line: 801

Fatal error:
Something is wrong in the coordinate formatting of file system.gro. Note
that gro is fixed format (see the manual)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I am not able to understand that in system.gro file do we have to do the
change in the no of atoms according to the inflated_system.gro file or not.
Another thing is if i am adding Chloride ions to equalize the charge do i
have to reduce the no of POPC molecules or not. Kindly suggest what should
be done i looked into the system.gro file and also the line it is referring
to i did not find anything unusual. But there is a catch its the same
molecule LEU which was having link to NH3.

Please suggest what should be done.

Thanks in advance.


On Wed, Feb 27, 2013 at 8:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/27/13 10:03 AM, swati rana wrote:
>
>> Hi all,
>>
>> After running the following command
>> <b>perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5
>> area.dat</b>
>>   I modified the lipids in the topol.top file and in system.gro file the
>> no
>> of lipids and no of atoms respectively.
>>
>> but after that for energy minimization when i ran the following command:
>> <b>grompp -f EM.mdp -c system.gro -p topol.top -o em.tpr</b>
>>
>> It is showing the following error. Please tell me if the command is right
>> or not and if it is right then what can be done to resolve and why exactly
>> it is showing this error. I checked the topology file but i am not able to
>> reach any conclusion. Please guide me as most of you have faced this error
>> and got the solution for it .
>>
>>
>> <b>Ignoring obsolete mdp entry 'title'
>>
>> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
>> Generated 867 of the 1891 non-bonded parameter combinations
>> Excluding 3 bonded neighbours molecule type 'Protein'
>> Excluding 3 bonded neighbours molecule type 'POPC'
>> Excluding 2 bonded neighbours molecule type 'SOL'
>>
>> NOTE 1 [file topol.top, line 21239]:
>>    System has non-zero total charge: 3.000002
>>    Total charge should normally be an integer. See
>>    http://www.gromacs.org/**Documentation/Floating_Point_**Arithmetic<http://www.gromacs.org/Documentation/Floating_Point_Arithmetic>
>>    for discussion on how close it should be to an integer.
>>
>>
>>
>>
>> ------------------------------**-------------------------
>> Program grompp, VERSION 4.5.5
>> Source code file: /build/buildd/gromacs-4.5.5/**src/kernel/grompp.c,
>> line: 523
>>
>> Fatal error:
>> number of coordinates in coordinate file (system.gro, 10019)
>>               does not match topology (topol.top, 17093)
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors>
>> </b>
>>
>>
> Did you consult the website?  The answer is always the same...
>
> If the numbers don't match, then your bookkeeping was incorrect.  Your
> topology specifies more atoms than your coordinate file, so you did not
> correctly account for the deletion of lipids or water.  Note that above,
> grompp is looking for SOL, but InflateGRO deletes all solvent from the
> input file, so you need to remove them from your topology as well.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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