Hello,
I am running g_covar. But the program halts with the error message that
the given xtc file was not found.
In fact the xtc file which is 7.1GB was very much existing. I suppose
that it is a case of large file.
I compiled GROMACS3.1.4 with --enable-largefile. But still the same
error occurs. How to make g_covar
recognise this file?
##########################################################################
:-) G R O M A C S (-:
GRoups of Organic Molecules in ACtion for Science
:-) VERSION 3.1.4 (-:
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.
:-)
/users/sridhar/bin/GROMACS314_SOLARIS/SERIAL/sparc-sun-solaris2.9/ultrasparc3/bin/g_covar
(-:
Option Filename Type Description
------------------------------------------------------------
-f 50NS_WT.xtc Input Generic trajectory: xtc trr trj gro
g96 pdb
-s ../FILES/b4md_1cyp_WT.tpr Input Structure+mass(db): tpr
tpb tpa
gro g96 pdb
-n ../FILES/pr_1cyp_WT.ndx Input, Opt! Index file
-o eigenval_WT.xvg Output xvgr/xmgr file
-v eigenvec_WT.trr Output Full precision trajectory: trr trj
-av average_WT.pdb Output Generic structure: gro g96 pdb
-l covar_WT.log Output Log file
-xpm covar.xpm Output, Opt. X PixMap compatible matrix file
-xpma covara.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 0 Set the nicelevel
-b time 12000 First frame (ps) to read from trajectory
-e time 50000 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]fit bool yes Fit to a reference structure
-[no]ref bool no Use the deviation from the conformation in the
structure file instead of from the average
-[no]mwa bool no Mass-weighted covariance analysis
-last int -1 Last eigenvector to write away (-1 is till the
last)
Reading file ../FILES/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision)
Reading file ../FILES/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision)
Choose a group for the least squares fit
Group 0 ( System) has 41820 elements
Group 1 ( Protein) has 4858 elements
Group 2 ( Protein-H) has 3775 elements
Group 3 ( C-alpha) has 478 elements
Group 4 ( Backbone) has 1434 elements
Group 5 ( MainChain) has 1913 elements
Group 6 (MainChain+Cb) has 2361 elements
Group 7 ( MainChain+H) has 2363 elements
Group 8 ( SideChain) has 2495 elements
Group 9 ( SideChain-H) has 1862 elements
Group 10 ( Prot-Masses) has 4858 elements
Group 11 ( Non-Protein) has 36962 elements
Group 12 ( HEME) has 47 elements
Group 13 ( SOL) has 36912 elements
Group 14 ( CL-) has 3 elements
Group 15 ( Other) has 36962 elements
Group 16 (Protein_HEME) has 4905 elements
Group 17 (Protein_HEME_CL-) has 4908 elements
Select a group: 3
Choose a group for the covariance analysis
Group 0 ( System) has 41820 elements
Group 1 ( Protein) has 4858 elements
Group 2 ( Protein-H) has 3775 elements
Group 3 ( C-alpha) has 478 elements
Group 4 ( Backbone) has 1434 elements
Group 5 ( MainChain) has 1913 elements
Group 6 (MainChain+Cb) has 2361 elements
Group 7 ( MainChain+H) has 2363 elements
Group 8 ( SideChain) has 2495 elements
Group 9 ( SideChain-H) has 1862 elements
Group 10 ( Prot-Masses) has 4858 elements
Group 11 ( Non-Protein) has 36962 elements
Group 12 ( HEME) has 47 elements
Group 13 ( SOL) has 36912 elements
Group 14 ( CL-) has 3 elements
Group 15 ( Other) has 36962 elements
Group 16 (Protein_HEME) has 4905 elements
Group 17 (Protein_HEME_CL-) has 4908 elements
Select a group: 3
Note: the fit and analysis group are identical,
while the fit is mass weighted and the analysis is not.
Making the fit non mass weighted.
Constructing covariance matrix (1434x1434)...
Fatal error: File 50NS_WT.xtc not found
#################################################################################
--
Sridhar Acharya, M
Senior Research Fellow
Lab of Computational Biology
CDFD, Gandipet Campus
Hyderabad. AP. INDIA
http://www.cdfd.org.in
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
[EMAIL PROTECTED]
Phone: Lab: +91-8413-235467*2044
Home: +91-40-27505833
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