Re: [gmx-users] pdb2gmx Warning: Long Bond

2012-05-16 Thread 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

[gmx-users] pdb2gmx Warning: Long Bond

2012-05-16 Thread Lara Bunte
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