On Tue, 2014-02-04 at 14:01 +0100, Anselm Horn wrote:
> Dear all,
>
> in the present version of cpptraj, there exists the possibility to
> compute a linear interaction energy between two entities in a very
> convenient way. The lie command then gives vdW and electrostatic
> contributions.
>
> In the AmberTools manuals, however, there is no further literature
> reference. Does lie use the normal Amber energy function (with the
> parameter set present in the top file) to compute the vdW energy?
The LIE energy in cpptraj uses the standard potential form for the
Lennard-Jones, but a rather atypical (for Amber) force- and
energy-shifted form for the electrostatic interactions (the formula is
shown in the AmberTools 13 manual for the lie action). No long-range
correction (either dispersion or electrostatic) is used by cpptraj.
However, the LIE method reports on differences between the local
environments of the ligand in a protein and solvent environment so the
exclusion of long-range effects and shifting of the electrostatic
potential are unlikely to be detrimental (especially if the cutoff is
sufficiently large, like 12 A).
Also worth mentioning is the presence of a LIE (called LRT for 'linear
response theory') calculation option in sander. It is present in Amber
12, but not documented in the manual (I believe you can use it by
specifying "ilrt=1" and "lrtmask" in the &cntrl section of the input
file -- lrtmask is analogous to the <Ligand Mask> option in cpptraj).
The sander implementation actually evaluates the energy using the full
PME electrostatics with a uniform, long-range dispersion correction. (I
only implemented the LIE action in cpptraj because I was unaware of its
presence in sander.) I've never used the sander implementation, so I'm
not sure if ilrt/lrtmask input is all you need, nor do I know in what
form the output will be (probably in the mdout file in some way).
> What would be the recommended citation for this feature?
> Just a reference to the AmberTools?
There's a cpptraj citation given at the end of every cpptraj run:
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
Theory Comput., 2013, 9 (7), pp 3084-3095.
That is sufficient.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 04 2014 - 06:00:02 PST
