[gmx-users] Problem using gromacs

[Justin Lemkul]

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.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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