[gmx-users] order of atoms in pdb-file

[David]

On Sun, 2004-01-11 at 19:39, Mr.Sridhar wrote:
> Dear gromacs users,
> 
> I faced this problem while running g_chi.
> 
> I wanted to calculate the the number of violations of ramachandran angles
> of the structures in trajectory file.
> The program outputs residue wise files of violations, that was fine. but
> there were error messages saying

You need files for the -s -f flags to match (in order of atoms).



> 
> "No chi1 & chi2 angle for ALA356 "
> 
This is correct

> and so on for almost all residues.
> 
Not correct probably

> When I observed one of the pdb file of one of the snapshots(I worte it
> with trjconv), I found that the order of atoms (backbone and sidechain
> atoms) in residues does not match the standard pdb format. For example,
> 
> #############order in gromacs pdb file################################
> ATOM   4754  N   VAL   469      52.310  49.270  35.790  1.00  0.00
> ATOM   4755  H   VAL   469      51.440  49.270  35.300  1.00  0.00
> ATOM   4756  CA  VAL   469      53.460  48.600  35.170  1.00  0.00
> ATOM   4757  CB  VAL   469      53.170  47.120  34.910  1.00  0.00
> ATOM   4758  CG1 VAL   469      54.410  46.380  34.390  1.00  0.00
> ATOM   4759  CG2 VAL   469      52.690  46.340  36.140  1.00  0.00
> ATOM   4760  C   VAL   469      53.740  49.280  33.840  1.00  0.00
> ATOM   4761  O   VAL   469      52.960  49.690  32.980  1.00  0.00
> 
> ###############order in a standard pdb file##############################
> ATOM    219  N   VAL A  60      19.146  69.476  49.828  1.00 43.93
> ATOM    220  CA  VAL A  60      18.468  69.172  51.091  1.00 39.04
> ATOM    221  C   VAL A  60      17.398  68.085  51.001  1.00 40.95
> ATOM    222  O   VAL A  60      17.209  67.353  51.969  1.00 36.94
> ATOM    223  CB  VAL A  60      17.888  70.420  51.791  1.00 39.98
> ATOM    224  CG1 VAL A  60      18.437  71.732  51.199  1.00 38.84
> ATOM    225  CG2 VAL A  60      16.378  70.406  51.791  1.00 39.59
> 
There is no standard order in pdb files AFAIK. And if there is then no
one seems to care. If you pdb2gmx then gromacs reorders the atoms (and
outputs optionally a file called clean.pdb). Maybe you can try that in
g_chi.



> 
> Is this the reason for error message in g_chi ?
> 
> When I checked the starting pdb file I used for running dynamics it
> contained the same order as that given by gromacs (above).
> 
> Does this affect the analysis of other properties or the dynamics run
> itself ?
See first answer.
> 
> Waiting for your suggessions.
> 
> 
> sridhar.
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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