[gmx-users] fitting

David van der Spoel spoel at xray.bmc.uu.se
Thu May 23 22:43:37 CEST 2002

On Thu, 23 May 2002 rams at poori.biochem.uiowa.edu wrote:

>Hello All,
>This is driving me crazy.
>I have a pdb file that I generate from a gro file of a protein.
>I have a 1ns trr file and the tpr file from there.
>I want to fit all the structures from the tpr file on to the pdb file I
>already have.
>It says in the manual that you can use g_rms or trjconv to fit to a
>reference structure.  How do i say what the reference structure is

If you want to get a new trajectory you do
trjconv -s file.pdb -f traj.trr -fit -o newtraj

or if you just want to compute the rmsd you do
g_rms -s file.pdb -f traj.trr

>S. Ramaswamy
>Department of Biochemistry.
>University of Iowa.
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>gmx-users at gromacs.org
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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