[gmx-users] pdb2gmx Warning: Long Bond

Lara Bunte lara.bunte at yahoo.de
Wed May 16 09:50:09 CEST 2012


If I use pdb2gmx -f mymol.pdb -water tip3p (CHARMM27 force field) I got warnings like this:

Making bonds...
Warning: Long Bond (1-2 = 0.261872 nm)
Warning: Long Bond (2-4 = 0.267812 nm)
Warning: Long Bond (6-4 = 0.260531 nm)

and so on....

For what problem tries GROMACS to warn me? Should I change something? 

In my .rtp parametrization file in the CHARMM27 folder I gave the equilibrium bond length in angstrom with corresponding force constant in kcal/mol, that are out of a supporting Information of a group, that made quantum mechanical calculations with my molecule. 

Thanks for help

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