[gmx-users] pdb2gmx does not recognize residues

[Kukol, Andreas]

Hello Rolf,

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.

Best wishes
Andreas

> -----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
> END
>
>
> 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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