Re: PCA Analysis of CGMD

From: Anirban (anirbang_at_cdac.in)
Date: Wed Apr 15 2009 - 15:42:44 CDT

Hi Josh,

Yes I tried with all combinations of groups like entire system also and
the same error happens. Ok, I will post this in Gromacs mail list once.
NAMD/VMD does'nt have any script to do PCA?

Thanks a lot,

On Wed, 2009-04-15 at 07:45 -0700, Joshua Adelman wrote:
> 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
> ------------------------------------------------------------------------------------------------------
>
>

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

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