[gmx-users] Fwd: Lysosyme in water

[Ommair Ishaque]

source .../gromacs.5.x/build/bin/GMXRC

Ommair

On Mon, Jun 5, 2017 at 12:45 AM, shivanigupta.gupta6 at gmail.com <
shivanigupta.gupta6 at gmail.com> wrote:

> Dear Gromacs
>
> I am new and a beginner to this system. I am trying to learn through
> tutorials for version 5. When i performed i got the following error .
> [shivani at POLY3 tut1]$ editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c
> -d 1.0 -bt cubic
> -bash: editconf: command not found
> [shivani at POLY3 tut1]$ gmx editconf -f 1AKI_processed.gro -o
> 1AKI_newbox.gro
> -c -d 1.0 -bt cubic
> -bash: gmx: command not found
> [shivani at POLY3 tut1]$ gmx_mpi  editconf -f 1AKI_processed.gro -o
> 1AKI_newbox.gro -c -d 1.0 -bt cubic
> -bash: gmx_mpi: command not found
> [shivani at POLY3 tut1]$ gmpp  editconf -f 1AKI_processed.gro -o
> 1AKI_newbox.gro -c -d 1.0 -bt cubic
> -bash: gmpp: command not found
> [shivani at POLY3 tut1]$ ls
> 1AKI.pdb  1AKI_processed.gro  posre.itp  topol.top
> [shivani at POLY3 tut1]$ ll
> total 812
> -rw-rw-r-- 1 shivani shivani 116316 Jun  1 15:24 1AKI.pdb
> -rw-rw-r-- 1 shivani shivani  98776 Jun  1 15:10 1AKI_processed.gro
> -rw-rw-r-- 1 shivani shivani  31304 Jun  1 15:10 posre.itp
> -rw-rw-r-- 1 shivani shivani 576928 Jun  1 15:10 topol.top
> [shivani at POLY3 tut1]$
>
> Can you help me in fixing the same .
>
> Thanks
> Regards
> Shivani
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