[gmx-users] pdb2gmx does not recognize residues
a.kukol at herts.ac.uk
Fri May 15 11:13:43 CEST 2009
There might be some issues with the exact format, below I pasted a record from a standard pdb-file (that works with pdb2gmx) for comparison.
Otherwise for a simple molecule like methane, x2top is probably better suited than pdb2gmx to generate the topology.
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Rolf Erwin Isele-Holder
> Sent: 15 May 2009 09:12
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pdb2gmx does not recognize residues
> 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
>From a working pdb-file:
> ATOM 676 O ILE A 40 23.416 2.231 -1.229 1.00 0.00 O
> 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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