[gmx-users] g_covar

[Berk Hess]

This is an incorrect warning, which has been introduced in
version 3.3.2. I have corrected the warning for 3.3.3.

Berk.

> Date: Wed, 9 Jan 2008 14:51:52 +0100
> From: tangxuan82 at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] g_covar
> 
> Dear all,
> When I am using g_covar to calculate the covariance matrix for alpha 
> carbons in one subunit of my protein, I get a warning" WARNING number of 
> atoms in tpx (929) and trajectory (293401) do not match". 929 is the 
> alpha carbon number and 293401 is  whole system atom number. In the 
> command, I used trr file and tpr file of the whole system. Do I have to 
> get a new trr file and tpr file just for these alpha carbons? 
> Some information  is shown below.
> "Group     0 (      System) has 293401 elements
> Group     1 (     Protein) has 75295 elements
> Group     2 (   Protein-H) has 38096 elements
> Group     3 (     C-alpha) has  4831 elements
> Group     4 (    Backbone) has 14493 elements
> Group     5 (   MainChain) has 19340 elements
> Group     6 (MainChain+Cb) has 23750 elements
> Group     7 ( MainChain+H) has 23963 elements
> Group     8 (   SideChain) has 51332 elements
> Group     9 ( SideChain-H) has 18756 elements
> Group    10 ( Prot-Masses) has 75295 elements
> Group    11 ( Non-Protein) has 218106 elements
> Group    12 (         KCX) has   184 elements
> .
> .
> Group   107 (chO_chV_&_C-alpha) has   929 elements
> Select a group: 107
> Selected 107: 'chO_chV_&_C-alpha'
> Calculating the average structure ...
> trn version: GMX_trn_file (single precision)
> Reading frame       0 time 20000.000  
> WARNING number of atoms in tpx (929) and trajectory (293401) do not match
> Last frame       1000 time 30000.000  
> 
> Last frame       1000 time 30000.000   to ./#average.pdb.17#
> Read 1001 frames
> 
> Trace of the covariance matrix: 2.34563 (nm^2)
> 100%
> Diagonalizing ...
> 
> Sum of the eigenvalues: 2.34563 (nm^2)
> 
> Writing eigenvalues to eigenval.xvg
> 
> Writing reference, average structure & eigenvectors 1--1000 to eigenvec.trr
> Wrote the log to covar.log"
> 
> Tang
> 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/