Catching up on 2 weeks of vacation emails, so I'm sorry if someone else
answered this already:
AMBER does support rhombic dodecahedral boxes (I believe a regular
dodecahedron is not space filling), but only in the framework of triclinic
coordinates. However LEAP does not, to my knowledge, support anything other
than orthorhombic and truncated octahedral coordinates at present. Thus,
you must manually set the lattice vectors in your crd file (a=b=c, alpha =
60, beta = 90, gamma = 60). When you use "set box" in LEAP (which you must
do so that PBCs are flagged in the prmtop?) you will essentially get
nonsense in those fields and will have to change them manually to what they
are "supposed" to be. I don't think AMBER will double check you on any of
this, so visualize often at the start to make sure things are sensible.
Technically there is also a box flag in the prmtop that should be changed,
but AMBER will recognize this at runtime and automatically change it.
Since the actual simulation is done in a triclinic system, the trajectories
you get back will probably not look like what you are expecting, even if you
use iwrap=0. PTRAJ can remedy this with the "familiar" flag, but the exact
commands probably depend on your system.
Hope that helps,
Brian
On Fri, Aug 5, 2011 at 2:08 AM, E. Nihal Korkmaz <enihalkorkmaz.gmail.com>wrote:
> Dear all,
>
> Does Amber have a dodecahedron box for solvation? I know there is
> octahedron
> but but dodeca- is close to spherical so would result in a same number of
> cuttoff and of course i'd prefer that :)
>
> Thanks,
> --
> Elif Nihal Korkmaz
>
> Research Assistant
> University of Wisconsin - Biophysics
> Member of Qiang Cui & Thomas Record Labs
> 1101 University Ave, Rm. 8359
> Madison, WI 53706
> Phone: 608-265-3644
> Email: korkmaz.wisc.edu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Thu Aug 25 2011 - 09:00:04 PDT
