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

swati rana swati.rana088 at gmail.com
Sat Mar 2 07:42:06 CET 2013


Hi Justin,

Thanks a lot, that suggestion of yours helped. I am on the equilibration
step and its running but nothing is happening on the terminal its just
stagnant. Is it fine because its more than 17 hrs now. Is there some
problem.
After running the second command nothing is happening on the terminal.

grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr

mdrun -deffnm nvt

I am sorry as it is not a reasonable question to ask but i am just asking
out of curiosity and lack of time.

Thanks in advance.



On Wed, Feb 27, 2013 at 10:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/27/13 11:14 AM, swati rana wrote:
>
>> 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<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.
>>
>
> No, the number of atoms in the coordinate file should be correct.
>  InflateGRO does this for you.
>
>
>  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
>>
>
> During inflation and shrinking, you should not be adding solvent or ions.
>  You will get a nonsensical result.
>
>
>  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.
>>
>>
> Probably a visualization artifact.  Real bonds are set in the topology,
> not in whatever the visualization program guesses.
>
>
> -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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