[gmx-users] endcapping

w.j.schravendijk at students.pharm.uu.nl w.j.schravendijk at students.pharm.uu.nl
Mon Feb 18 14:34:46 CET 2002

I edited the pdb to include the terminal N into the last residue (instead
of being a residue of its own) and it worked, using -nosort and -ter as
options to pdb2gmx. -nosort was necessary, while gromacs would have forced
a carboxyl end to it otherwise.

Thanks for helping!

There is a NH2 in the n-terminal database, but in this case a NH2 group at
the c-terminal was needed, which isn't present (sorry for creating a
misunderstanding at this point).

N-terminus: None
Select C-terminus type (end)
 0: None
 1: COO-
 2: COOH

> > pdb2gmx gives the error: no alpha carbon present in residue 27.
> Can't find that error message in the source code.
> Which version of GROMACS are you using?

The actual error was this (gromacs 3.0):
Fatal error: atom C not found in residue 27NH2 while combining tdb and rtp

> > I would also like to label that residue, I guess that requires the same
> > steps?
> ?label? what do you mean with that?

I meant: Add a fluorescent molecule in place of the NH2 at the end. I
guess the solution for that will be something silimar to this NH2 problem,
so it should be possible.

Greetings, Pim

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