[gmx-users] Re: Dihedral Question

[Fabian Casteblanco]

Thanks Justin for your help :-)

Best regards,
Fabian Casteblanco

On Fri, Aug 5, 2011 at 11:46 AM, Fabian Casteblanco
<fabian.casteblanco at gmail.com> wrote:
> 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
>



-- 
Best regards,

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