[gmx-users] pdb2gmx Problems

[Gary]

Hi David

I've been reading chapter 5, but I'm still unsure
about a few things...

How do you derive the values for these topology files?
(e.g. charges, dihedrals, bonds)  are there any source
that provide (some of) this information.

Thank You Again.

-Gary


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