[gmx-users] g_cluster for concoord output?

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Apr 3 08:34:48 CEST 2012

Hi Albert,

pdb is mentioned valid input for both -f (trajectory) and -s
(reference). So you can use the file you have for both:

g_cluster -s disco.pdb -f disco.pdb [...]



On Tue, Apr 3, 2012 at 8:23 AM, Albert <mailmd2011 at gmail.com> wrote:
> Dear:
>    I've generated a disoc.pdb file by concoord and does any one have any
> idea how to analyze it by Gromacs g_cluster? when I read the manual of
> g_cluter, it will require
>  -f       traj.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
>  -s      topol.tpr  Input, Opt.  Structure+mass(db): tpr tpb tpa gro g96 pdb
>  -n      index.ndx  Input, Opt.  Index file
>  -dm       rmsd.xpm  Input, Opt.  X PixMap compatible matrix file
> but the concoord output is a single pdb file.....
> thank you very much
> best wishes
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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