[gmx-users] problem regarding installation of gromacs-4.5.5

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 15 13:56:07 CEST 2012

On 6/15/12 7:37 AM, Nidhi Jatana wrote:
> Dear Sir/Madam
> This is Nidhi Jatana. I downloaded the lastest version of gromacs i.e. 4.5.5
> from the link (ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz) and have
> installed it but whenever I am trying to run any of the programs, its showing me
> the version to be 4.0.5. For example, I was trying to run the lysozyme tutorial
> and while running genion i gave in the command:
> genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8
> and getting this as the output (not posted the entire output)
>                           ":-)  G  R  O  M  A  C  S  (-:
>             Glycine aRginine prOline Methionine Alanine Cystine Serine
>                              :-)  VERSION 4.0.5  (-:"
> I have installed it thrice, but the problem persists. Infact, I am getting an
> error (Fatal error: No such moleculetype NA) while running minimization. And
> when I saw the user-mailing lists, it shows me that there is some problem with
> the version. What should I do? Should I install the previous version?

Likely you have an existing version of Gromacs on whatever system you are 
working on, and the new version you are trying to install isn't being 
recognized.  You should locate the existing (4.0.5) installation with:

which genion (or any other Gromacs program name)

Likely your shell environment is configured to use this location by default 
(i.e. it is in your $PATH).  You haven't posted the commands for how you tried 
to install Gromacs-4.5.5, and you may also have to modify your environment to 
find it, but you need to deal with the existing (old) version first to avoid 
confusion.  Then follow:




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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