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

MGiò magiofer at gmail.com
Wed Sep 28 14:57:19 CEST 2005

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
good luck!


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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