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

[Alan Dodd]

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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