[gmx-users] pdb2gmx does not recognize residues

Nuno Azoia nazoia at det.uminho.pt
Fri May 15 12:30:18 CEST 2009


I think this a problem of bad format of your pdb file.
What is happening is that your CH4 is not in the right position, in the
pdb file, so pdb2gmx are just reading the letter C from your CH4.
Check carefully the pdb file format. You can try to remove two empty
spaces between ATOM and the residue number. It should work. But again,
check the pdb file format, or just use some software to write the pdb
for you. You can use Pymol, for example, and then just rename the

Nuno Azoia 

On Fri, 2009-05-15 at 10:11 +0200, Rolf Erwin Isele-Holder wrote:
> 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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Nuno Gonçalo Azoia Lopes
Finishing Research Laboratory
Textile Engineering Department
Universidade do Minho
Campus de Azurém
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E-mail: nazoia at det.uminho.pt

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