[gmx-users] gromacs error

[Justin Lemkul]

On 9/22/14 10:14 AM, Yaser Hosseini wrote:
> hi guys i have a problems with gromacs command .how can i can solve
> this problems:
> i install gromacs and i dont know what can i do:
>
>
> gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
> No command 'gmx' found, did you mean:
>   Command 'gcx' from package 'gcx' (universe)
>   Command 'ngmx' from package 'gromacs' (universe)
>   Command 'gm' from package 'graphicsmagick' (universe)
>   Command 'gmt' from package 'libgenome-perl' (universe)
> gmx: command not found
>

You haven't configured your environment properly.

http://www.gromacs.org/Documentation/Installation_Instructions#getting-access-to-gromacs-after-installation

>
> and other problem :
>
> solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top
> solvate: command not found
>

That's not a valid command.  "gmx solvate" is, if you follow the instructions above.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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