[gmx-users] pdb2gmx Warning: Long Bond

[Mark Abraham]

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.

Mark