[gmx-users] calculate torsional energy of the ligand from thetrajectory (fwd)

[Nancy Deng]

Dear All,

I am trying to get cluster analysis from a 5ns MD trajectory by the
following command:
    g_cluster_mpi -f 5ns.xtc -s system500ps.gro -n index.ndx -o
rmsd-cluster -g cluster.log -tr cluster-trans -dt 10 -cutoff 0.1 -method
jarvis-patric

At the last step, it shows the below fatal error:

    Writing rms distance/clustering matrix Fatal error: Can not plot more
than 16 discrete colors

Could anyone please help???

thanks,

nancy

----- Original Message ----- 
From: "David van der Spoel" <spoel at xray.bmc.uu.se>
To: <gmx-users at gromacs.org>
Sent: Tuesday, May 03, 2005 11:35 AM
Subject: Re: [gmx-users] calculate torsional energy of the ligand from
thetrajectory (fwd)


> Date: Tue, 3 May 2005 20:12:32 +0200
> From: Minami Mo <minami.mo at gmail.com>
> To: David <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] calculate torsional energy of the ligand from the
>     trajectory
>
> David,
>
> >Sorry, can you say explain a bit more? What I understand from you is
> >to modify the topology file .top (remove the protein), run "grompp"
> >and "mdrun -rerun" again.  I tried this, but after I removed the
> >protein from the toplogy file and run grompp, it prompts out this
> >error:
>
> You just want to remove the dihedrals from the topology not the rest of
> the protein.
>
>
> David.
>
>
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