On Wed, Nov 14, 2012 at 5:09 AM, Joakim Jämbeck <joakim.jambeck.mmk.su.se>wrote:
> Hi,
>
> Does anybody know if it is possible to assign special 1-4 van der Waals
> interactions in Amber?
>
Only if you use the CHARMM force field through the chamber program.
Hence, I would like to scale some of the 1-4 interactions by a factor as
> done in most of the Amber FFs but some of them I would like to assign a
> special Lennard-Jones parameters to, for instance between two sp3 carbons.
>
This cannot be done without changing the code. All of the pieces of the
code are in place so all you'll have to do is adjust some subroutine calls
in key places. For instance, sander and pmemd already have code in place
to deal with different 1-4 and nonbonded VDW terms (since that's how the
CHARMM force field works). It also has code in place to do variable 1-4
scaling, so all you would need to do is assign the 1-4 VDW parameters
'correctly' (i.e., those that should be different take different values and
those that should be the same should take the same values as the
LENNARD_JONES_ACOEF and LENNARD_JONES_BCOEF arrays). Then you'll need to
assign the 1-4 scaling arrays to scale those dihedrals that you want to
scale.
In summary, you will have to do a little bit of coding, and you will need
to know the details of the topology file well enough to modify it (ParmEd
can help here) to add the information that you need. However, you will not
have to add any code that calculates potentials or forces -- just code to
adjust the topology file, set the correct data structures, and call the
appropriate subroutines. For someone just getting started with Amber,
though, I would not expect it to be a 'quick' process, even if you're
familiar with Fortran90 programming.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Nov 14 2012 - 05:30:03 PST
