Re: PCA Analysis of CGMD

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Wed Apr 15 2009 - 09:45:53 CDT

Hi Anirban,

It's really hard to determine what's going on when you get a
segmentation fault error like that. Do you still get the error when
you select different groups (say the entire system)? If errors
persist, I would say that these questions should probably be posted on
the gromacs' user list rather than here.

Josh

On Apr 15, 2009, at 12:44 PM, Anirban wrote:

> 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
>

------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
------------------------------------------------------------------------------------------------------

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