[gmx-users] Problem using gromacs

[masoud keramati]

in OPLS ff when i use tip3p  water  i got this error but if tip3p selected
then there no problem and it's interesting!

On Mon, Jan 4, 2016 at 2:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/4/16 4:27 AM, soumi  wrote:
>
>> Respected Sir,
>>                I am new user of gromacs. When I use the following command
>> gmx grompp -f ions.mdp -c 1aki_solv.gro -p topol.top -o ions.tpr
>>
>> I get the following error :Number of coordinates in coordinate file does
>> not match topology file.
>> Please tell me how can I correct the number of coordinates in gromacs?
>>
>>
>
> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>
> Since you've (presumably) already solvated the system, you probably forgot
> to let genbox adjust your topology for you via the -p option.  Based on
> your file naming, I assume you're following my lysozyme tutorial, which
> lays everything out exactly, so be sure you're using the exact commands and
> you know what each option is doing.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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