[gmx-users] pdb2gmx Problems

[Gary]

Hi David,

Thanks for all the guidance so far...

So what I need to do is create my own definition of
residues used in an .itp file?  ...and a good way of
doing that is to use prodrg?

Am I on the right track?

-Gary




--- David <spoel at xray.bmc.uu.se> wrote:
> On Tue, 2004-07-13 at 19:56, Gromacs Newbie wrote:
> > So pdb2gmx doesn't work for non-protein molecules?
> > 
> That's almost correct. Check e.g. ffoplsaa.rtp for
> supported residues.
> > -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
> > > > 
> > > David.
> 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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