[gmx-users] pdb2gmx Problems

[David]

On Mon, 2004-07-12 at 22:33, Gromacs Newbie wrote:
> Hi All,
> 
> I'm trying to convert the following pdb file:
> HEADER    PROTEIN
> TITLE     (3,3) SWCNT
> AUTHOR    TubeGen 3.1, J T Frey, University of
> Delaware
> ATOM      1  C   UNK     1      -6.394   0.000  -1.231
>  1.00  0.00
> ATOM      2  C   UNK     1      -4.944   0.000  -1.231
>  1.00  0.00
> ATOM      3  C   UNK     1      -4.263   0.000   0.000
>  1.00  0.00
> ATOM      4  C   UNK     1      -2.812   0.000   0.000
>  1.00  0.00
> ATOM      5  C   UNK     1      -2.132   0.000  -1.231
>  1.00  0.00
> ATOM      6  C   UNK     1      -0.681   0.000  -1.231
>  1.00  0.00
> ATOM      7  C   UNK     1       0.000   0.000   0.000
>  1.00  0.00
> ATOM      8  C   UNK     1       1.451   0.000   0.000
>  1.00  0.00
> ATOM      9  C   UNK     1       2.132   0.000  -1.231
>  1.00  0.00
> ATOM     10  C   UNK     1       3.582   0.000  -1.231
>  1.00  0.00
> ATOM     11  C   UNK     1       4.263   0.000   0.000
>  1.00  0.00
> ATOM     12  C   UNK     1       5.714   0.000   0.000
>  1.00  0.00
> MASTER        0    0    0    0    0    0    0    0  
> 12    0    0    0
> END
> 
> with the command:
> pdb2gmx -f c.pdb -o c.gro -p c.top
> 
> and I am getting the error message:
> Looking whether force field file ffG43a1.rtp exists
> Opening library file
> /usr/local/share/gromacs/top/ffG43a1.rtp
> Opening library file
> /usr/local/share/gromacs/top/aminoacids.dat
> Reading c.pdb...
> Warning: Number of atoms in c.pdb is 0
> ATOM', 0 atomsGen 3.1, J T Frey, University of
> Delaware
> Opening library file
> /usr/local/share/gromacs/top/xlateat.dat
> 23 out of 23 lines of xlateat.dat converted
> succesfully
> Fatal error: No atoms found in pdb file c.pdb
> 
> Can anyone tell me what is wrong with my file c.pdb?

It's not a protein!

For stuff like this you are better off with the prodrg server, or if all
else fails x2top.
> 
> Thanks in advance.
> 
> -Gary
> 
> 
> 		
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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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