On Fri, Oct 4, 2013 at 7:52 AM, CHAMI F. <fatima.chami.durham.ac.uk> wrote:
> Dear Jason,
>
> I have downloaded AmberTools 13 and I looked in the manual. I would like
> to change the scaling factor scnb
> on some part of my system: let say the rigid and flexible part of my
> molecule have different scaling of VDW 1-4 interaction .using the
> following command in parmed ..
>
> Usage: changeLJ14Pair <mask1> <mask2> <Rmin> <epsilon>
>
This does not do what you think it does. The CHARMM force fields do not
scale 1-4 van der Waals interactions like the Amber force fields do.
Instead, 1-4 van der Waals interactions are computed as different atom
types with different vdW parameters altogether.
If you want to change the 1-4 scaling parameters in Amber, you need to use
the "scnb" and "scee" functions in ParmEd. However, ParmEd does not have
any way of changing individual 1-4 scaling parameters very easily (scnb and
scee change _all_ of the scaling parameters). You can delete an entire
dihedral and add it back term-by-term, specifying the new 1-4 scaling
parameters there if you want, but it will probably be much easier to
recreate the prmtop using tleap and change the 1-4 scaling parameters
inside your frcmod file instead.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 04 2013 - 07:30:07 PDT
