[gmx-users] Polyglycine PDB file.

[C Johnson]

I'm new to gmx so I'm just seeing if I'm able to make homoblock polypeptides.  I would like to simulate a 5 residue polyglycine.  I've used PRODRG to generate the pdb file, however trying to convert the file with pdb2gmx I receive the error:

Fatal error:
Residue 'Y' not found in residue topology database

My pdb file is:


ATOM    1  O   GLY     1      -2.600  -2.350  -0.400  1.00 20.00             O
ATOM    2  C   GLY     1      -2.250  -1.400   0.340  1.00 20.00             C
ATOM    3  O   GLY     1      -1.850  -1.490   1.520  1.00 20.00             O
ATOM    4  CA  GLY     1      -2.330   0.010  -0.240  1.00 20.00             C
ATOM    5  N   GLY     1      -3.620   0.630   0.130  1.00 20.00             N
ATOM    6  C   GLY     2      -3.800   1.640   1.000  1.00 20.00             C
ATOM    7  O   GLY     2      -4.910   2.110   1.230  1.00 20.00             O
ATOM    8  CA  GLY     2      -2.600   2.240   1.730  1.00 20.00             C
ATOM    9  N   GLY     2      -2.160   3.460   1.030  1.00 20.00             N
ATOM   10  C   GLY     3      -2.510   4.720   1.320  1.00 20.00             C
ATOM   11  O   GLY     3      -2.050   5.670   0.680  1.00 20.00             O
ATOM   12  CA  GLY     3      -3.510   4.990   2.460  1.00 20.00             C
ATOM   13  N   GLY     3      -4.640   5.790   1.950  1.00 20.00             N
ATOM   14  C   GLY     4      -5.930   5.680   2.300  1.00 20.00             C
ATOM   15  O   GLY     4      -6.800   6.390   1.810  1.00 20.00             O
ATOM   16  CA  GLY     4      -6.340   4.640   3.360  1.00 20.00             C
ATOM   17  N   GLY     4      -6.800   5.360   4.570  1.00 20.00             N
ATOM   18  C   GLY     5      -7.330   4.810   5.670  1.00 20.00             C
ATOM   19  O   GLY     5      -7.640   5.500   6.640  1.00 20.00             O
ATOM   20  CA  GLY     5      -7.550   3.300   5.730  1.00 20.00             C
ATOM   21  N   GLY     5      -8.990   3.000   5.660  1.00 20.00             N
END

I'm not sure what I could be doing wrong since I pretty much mimicked the speptide.pdb in the tutor file.

Thanks for the help,
Joe.
 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100912/70f95794/attachment.html>