[gmx-users] pdb2gmx does not recognize residues

Rolf Erwin Isele-Holder Rolf.Isele at rwth-aachen.de
Fri May 15 10:11:59 CEST 2009

Hello everybody,

I'm trying to set up a box with methane. Therefore I wrote a small pdb file which looks like this:

ATOM     1   CH4    CH4     1        1.0     1.0     1.0     1.0     0.0
ATOM     2   CH4    CH4     2        0.5     0.5     0.5     1.0     0.0 
ATOM     3   CH4    CH4     3        0.0     0.0     0.0     1.0     0.0 

Unfortunately when using bdb2gmx on this file, the message: " Residue 'C' not found in redsidue database" is shown.
Why does gromacs not recognize that it is not supposed to look for a residue called 'C' which does not exist, but a residue called 'CH4' which is contained in ffG43a1.rtp ?
Does anybody know the answer?

Greetings, Rolf

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