[gmx-users] Dihedral Question

[Fabian Casteblanco]

Hello all,

I'm having trouble finding information that explains the relationship
between 1,4 pair interactions and dihedrals.  I'm building a drug
molecule using CGenFF, and extension of CHARMM27 and since the drug is
a bit complex, it has several dihedral parameters that are missing.  I
ran them with the missing parameters and then I reran it with
estimated parameters based on other dihedral parameters for similar
dihedrals and they look somewhat similar but still have noticeable
differences.

>From what I understood, the 1,4 pair interactions should already be
setting most of the dihedral angles up and the dihedrals are simply
added energy consequences inorder to keep the specified torsion angle.
 Is this the correct way 1,4 pair interactions and dihedrals work
together?  Also, if I were to simply run without using the dihedral
parameters, would it make a huge difference when extracting
themodynamics information from a mixture of this single drug molecule
in different types of solvent?

Thank you all for sharing your expertise.  It's greatly appreciated.

-- 
Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.casteblanco at gmail.com