[gmx-users] pdb2gmx error

[Mark Abraham]

Hi,

These errors mean exactly what they say. There's a mismatch between your
structure file and the residue structure in the database. So you need to
look at them both and see what is wrong. Chapter 5 of the manual is your
friend.

Mark
On 19/03/2015 3:17 am, "RJ" <rajiv at kaist.ac.kr> wrote:

> Dear gmx,
>
>
> I tried to to use pdb2gmx and get this error for 3 to 4 residues. I even
> cleaned my crystal structure using Discovery studio/swissviewer which shows
> no error on it. I wonder, how do i rectify this problem ?
>
>
> WARNING: WARNING: Residue 1 named MET of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom H used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
> WARNING: WARNING: Residue 366 named LEU of a molecule in the input file
> was mapped
> to an entry in the topology database, but the atom O used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
> Before cleaning: 7060 pairs
>
>
> Residue 32681 named GLN of a molecule in the input file was mapped
> to an entry in the topology database, but the atom N used in
> an interaction of type improper in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
> --
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