[gmx-users] fitting
rams at poori.biochem.uiowa.edu
rams at poori.biochem.uiowa.edu
Thu May 23 21:54:21 CEST 2002
Ok! here I go first I try on the Linux box
---------
g_rms -s uq4_1.pdb -f 1ns_nr.trr
:-) G R O M A C S (-:
Giving Russians Opium May Alter Current Situation
:-) VERSION 3.1 (-:
Copyright (c) 1991-2002, University of Groningen, The Netherlands
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_rms (-:
Option Filename Type Description
------------------------------------------------------------
-s uq4_1.pdb Input Structure+mass(db): tpr tpb tpa gro g96
pdb
-f 1ns_nr.trr Input Generic trajectory: xtc trr trj gro g96
pdb
-f2 traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96
pdb
-n index.ndx Input, Opt. Index file
-o rmsd.xvg Output xvgr/xmgr file
-mir rmsdmir.xvg Output, Opt. xvgr/xmgr file
-a avgrp.xvg Output, Opt. xvgr/xmgr file
-dist rmsd-dist.xvg Output, Opt. xvgr/xmgr file
-m rmsd.xpm Output, Opt. X PixMap compatible matrix file
-bin rmsd.dat Output, Opt. Generic data file
-bm bond.xpm Output, Opt. X PixMap compatible matrix file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line
options
-nice int 19 Set the nicelevel
-b time -1 First frame (ps) to read from trajectory
-e time -1 Last frame (ps) to read from trajectory
-dt time -1 Only use frame when t MOD dt = first time (ps)
-tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h
-[no]w bool no View output xvg, xpm, eps and pdb files
-what enum rmsd Structural difference measure: rmsd, rho or
rhosc
-[no]pbc bool yes PBC check
-[no]fit bool yes Fit to reference structure
-prev int 0 Compare with previous frame
-[no]split bool no Split graph where time is zero
-skip int 1 Only write every nr-th frame to matrix
-skip2 int 1 Only write every nr-th frame to matrix
-max real -1 Maximum level in comparison matrix
-min real -1 Minimum level in comparison matrix
-bmax real -1 Maximum level in bond angle matrix
-bmin real -1 Minimum level in bond angle matrix
-nlevels int 80 Number of levels in the matrices
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
Opening library file /usr/local/share/gromacs/top/atommass.dat
Opening library file /usr/local/share/gromacs/top/aminoacids.dat
Select group for least squares fit
Group 0 ( System) has 723 elements
Group 1 ( Protein) has 723 elements
Group 2 ( Protein-H) has 575 elements
Group 3 ( C-alpha) has 72 elements
Group 4 ( Backbone) has 216 elements
Group 5 ( MainChain) has 289 elements
Group 6 (MainChain+Cb) has 357 elements
Group 7 ( MainChain+H) has 360 elements
Group 8 ( SideChain) has 363 elements
Group 9 ( SideChain-H) has 286 elements
Select a group: 3
How many groups do you want to compare ? 1
OK. I will compare 1 groups
Select group for RMSD
Group 0 ( System) has 723 elements
Group 1 ( Protein) has 723 elements
Group 2 ( Protein-H) has 575 elements
Group 3 ( C-alpha) has 72 elements
Group 4 ( Backbone) has 216 elements
Group 5 ( MainChain) has 289 elements
Group 6 (MainChain+Cb) has 357 elements
Group 7 ( MainChain+H) has 360 elements
Group 8 ( SideChain) has 363 elements
Group 9 ( SideChain-H) has 286 elements
Select a group: 3
Warning: can not make broken molecules whole without a run input file,
don't worry, mdrun doesn't write broken molecules
trn version: GMX_trn_file
Reading frame 0 time 0.000 Fatal error: Numerical Recipes: Too
many iterations in routine JACOBI
---------------------------
Then I try the trjconv and I end up the
trjconv -s uq4_1.pdb -f 1ns_nr.trr -fit -o newtraj
....
....
rn version: GMX_trn_file
Reading frame 0 time 0.000
Setting output precision to 0.001 (nm)
Back Off! I just backed up newtraj.xtc to #newtraj.xtc#
Fatal error: Numerical Recipes: Too many iterations in routine JACOBI
----
similar problems when I run on Compaq True64....
.....
Beleive me i did think it was this simple and I tried both already...
Thanks.
Rams.
> 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
>
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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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--
S. Ramaswamy
Department of Biochemistry.
University of Iowa.
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