Re: PCA Analysis of CGMD

From: Anirban (anirbang_at_cdac.in)
Date: Wed Apr 15 2009 - 14:44:29 CDT

Hello Josh and Rogan,

Thanks a lot for the help. I tried the way to do PCA that you said, but
I am getting the following error:
-----------------------------------------------------------------------
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
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/gromacs/share/gromacs/top/atommass.dat
Warning double different entries ASN ND 16.0227 and 144.24 on line 134
in file atommass.dat
Using last entry (16.0227)
Warning double different entries GLN NE 16.0227 and 20.1797 on line 140
in file atommass.dat
Using last entry (16.0227)
Warning double different entries HISA NE 14.0067 and 16.0227 on line 144
in file atommass.dat
Using last entry (14.0067)
Warning double different entries HISB ND 14.0067 and 16.0227 on line 145
in file atommass.dat
Using last entry (14.0067)
Warning double identical entries for HIS1 NE 14.0067 on line 146 in file
atommass.dat
Entries in atommass.dat: 173
WARNING: vdwradii 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/gromacs/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
Entries in elements.dat: 218

Choose a group for the least squares fit
Group 0 ( System) has 45 elements
Group 1 ( TA) has 15 elements
Group 2 ( TB) has 15 elements
Group 3 ( TC) has 15 elements
Group 4 (a_15_a_30_a_45) has 3 elements
Select a group: 4
Selected 4: 'a_15_a_30_a_45'

Choose a group for the covariance analysis
Group 0 ( System) has 45 elements
Group 1 ( TA) has 15 elements
Group 2 ( TB) has 15 elements
Group 3 ( TC) has 15 elements
Group 4 (a_15_a_30_a_45) has 3 elements
Select a group: 4
Selected 4: 'a_15_a_30_a_45'

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.

Calculating the average structure ...
Segmentation fault
-------------------------------------------------------------------------
I also tried by changing the aminoacids.dat file used by GROMACS, but
still the same error. Do I need to change any other file? How to
overcome this problem? Thanks in advance.

Regards,

-- 
Anirban Ghosh
Grade Based Engineer
Bioinformatics Team
Scientific & Engineering Computing Group
Centre for Development of Advanced Computing
Pune, India

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