[gmx-users] pdb2gmx Problems

[Gromacs Newbie]

So pdb2gmx doesn't work for non-protein molecules?

-Gary


--- David <spoel at xray.bmc.uu.se> wrote:
> 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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