[gmx-users] PDB2GMX warnings

[T.A.Wassenaar at chem.rug.nl]

Hi Davide,

You should probably not throw your bilayers through pdb2gmx as Xavier
said. The long bonds arise because pdb2gmx stitches everything together,
i.e. it makes one chain if there are no TER records or changes in the
chain identifier. So in your case lipids are bonded which are more than a
bond length apart (long bond) and which should not be bonded at all of
course. Usually getting a warning of a long bond means that the topology
file you got is no good.

Hope it helps,

Tsjerk

 On Mon, 16 Feb 2004 davide.demiliano at fastwebnet.it wrote:

> I've just started using GROMACS software for the first time to simulate
> a small lipid bilayer. When I try to create my .gro file using pdb2gmx a
> get several long bond warnings! What dose it mean exactly? (a ectually get
> my .gro file at the end of the process and the .pdb file I use it's already
> been used for other simulations). Thanks for your help
>
> Dr Davide D'Emiliano
> phd student
> Physics department
> Universita' degli studi di Roma "La Sapienza"
> Rome, Italy
>
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