[gmx-users] pdb2gmx Warning: Long Bond

Mark Abraham Mark.Abraham at anu.edu.au
Wed May 16 09:55:07 CEST 2012

On 16/05/2012 5:50 PM, Lara Bunte wrote:
> Hi
> 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?

That depends whether your molecule should have bonds this long in the 
configuration you provided to pdb2gmx... but since you've kept the 
nature of your molecule a mystery, you'll have to answer that yourself :-)

> 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.

See chapter 2 for the acceptable gromacs units. These do not include 
Angstrom or kcal/mol.


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