Dear All,
I have the coordinates i need to calculate the VDW+ELEC component alone for
each step. with amber ff vdw radii and charges. I have made a file
containing the radii, charge and Espilon values. along with all-with-all
interatomic distance.
But i am not sure who to go about from here
E= vDW _E+ ELEC_E
VDW_E=?
ELEC_E=?
I am using the equation given below. say form any two atom A and B
$epsi_total=sqrt($epsiA*$epsiB);
$Rzero= $vdwradiiA+$vdwradiiB;
$vdw= 4*$epsi_total*((1/4*(($Rzero/$AB_dist)**12)) -
(1/2*($Rzero/$AB_dist)**6));
For Electrostatic calculation,
$elec=((18.22)**2)*($chargA*$chargB)/$AB_dist,
Please let me know if this is OK.
Regards
Bergy
On Tue, Apr 30, 2013 at 6:50 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Apr 30, 2013, BERGY wrote:
>
> > I have generated DNA base steps wit different conformations.( step
> > parameter value combination (twist,roll and slide values) in PDB format..
> > The hbond occur between the base in the base pairs
> > and stacking occurs between base pairs. additionally the vdw and other
> > non-bonded interactions occurs. i would like to calculate these
> interaction
> > and potential energy.
>
> See if the analysis tools at w3dna.rutgers.edu do what you want.
>
> ...dac
>
>
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Received on Wed May 01 2013 - 15:00:02 PDT
