[gmx-users] pdb2gmx Problems

[David]

On Tue, 2004-07-13 at 22:48, Gary wrote:
> 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?
Yes, or read chapter 5 from the manual and do it yourself. Very
instructive.
> 
> -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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-- 
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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