Re: PCA Analysis of CGMD

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Wed Apr 15 2009 - 11:20:39 CDT

Hi, I have previously observed seg faults in the Gromacs analysis
tools when you provide them an index file whose indices refer to the
complete "topology" (i.e. the file provided with -s) but you're
feeding them a trajectory with a subset of atoms.

You should first make sure that the "topology" (-s file) has the same
number of atoms of the trajectory (-f file), and also that the numbers
in the index file range accordingly from 1 to 45 in this case (and NOT
from 1 to the size of the original complete system). If you generated
the index file on a pdb of the complete system, you need to repeat the
process on the reduced system.

Giacomo

---- -----
 Giacomo Fiorin
   Center for Molecular Modeling at
     University of Pennsylvania
     231 S 34th Street, Philadelphia, PA 19104-6323
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 mail: giacomo.fiorin_<at>_gmail.com
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---- ----

On Wed, Apr 15, 2009 at 10:45 AM, Joshua Adelman <jadelman_at_berkeley.edu> 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
> ------------------------------------------------------------------------------------------------------
>
>
>
>

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