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
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