[gmx-users] pdb2gmx --- fatal error- .gro file not created

[Fernando Mattio]

 Mgio you were right, my topology file is empty. However I could generate
the .gro file (that seems to be ok) with editconf. Well now the problem is
how to have the topology file... Residue 38 C is the problem, but I also
think it should not exist! As I am new as Gromacs user I don´t know what I
have to do to correct my topology file... I tried the -inter and -ter
options as Dodd wrote, but it was not clear for me how to use them
correctly, so it did not work. Do I have to specify none only fot the C
residue? More information about this would be great, thank you very much in
advance!
Fernando Mattio
2005/9/28, Alan Dodd <anoddlad at yahoo.com>:
>
> Residue 38 is probably a C-terminal amidation, and
> should not have a C in it anyways. I had the same
> problem with my peptide... use the option -inter, or
> -ter (specifying none at the interactive prompt for
> the c-terminus), to see if you can persuade gromacs to
> realise it's just a terminal residue. If that doesn't
> work, you may need to tinker with the terminus files
> in share/top. Make sure you examine any .gro file
> produced to be sure there's still the amidation there.
>
> --- MGiò <magiofer at gmail.com> wrote:
>
> > it is possible that residue 38 is not complete in
> > your structure, in
> > particular it has no C atom in its backbone, so the
> > tompology cannot be
> > written for that atom, have you checked if the .top
> > file is complete?
> > the simplest thing you can try to obtain the
> > correspondent .gro file from a
> > .pdb file is using editconf
> >
> > editconf -f input.pdb -o output.gro
> >
> > but I suspect thet, il the structure is not complete
> > editconf will stop
> > anyway.
> > good luck!
> >
> > Magiofer
> >
> >
> >
> > On 9/28/05, Fernando Mattio <mattiofer at gmail.com>
> > wrote:
> > >
> > > Dear Gromacs users,
> > >
> > > I started from a file 1WFA.pdb, and after using
> > the command
> > > pdb2gmx -f 1WFA.pdb -p WFA.top -o WFA.gro
> > > I expected to have the file WFA.gro
> > > However, this fatal error message appears: Fatal
> > error: atom C not found
> > > in residue 38NH2 while combining tdb and rtp
> > > Probably for this reason the file WFA.gro was not
> > created! But the WFA.top and
> > > the WFA_A.itp were created!
> > > I really would like to create this .gro file, once
> > I read this kind of
> > > file is better than the .pdb ... I don´t think the
> > command is wrong... and I
> > > started from a pdb file already created! So what
> > is the problem? How can I
> > > correct this?
> > > So please, if anyone knows what should I do to
> > have this .gro file it
> > > would be nice.
> > >
> > > Thank you very much in advance,
> > > Fernando.
> > >
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