Re: PCA Analysis of CGMD

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Wed Apr 15 2009 - 10:35:00 CDT

The tools are there to write a PCA analysis script in VMD using tcl,
but it might take some work to put it together especially if you then
want to generate structures along each of the modes, project
trajectories onto modes, etc.

Josh

On Apr 15, 2009, at 1:42 PM, Anirban wrote:

> 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,
>>>

------------------------------------------------------------------------------------------------------
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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