On Mon, Apr 04, 2005, Phineus Markwick wrote:
>
> This, of course gives a periodically repeating array of PL3 water molecules,
> rather than the periodically repeating equilibrated water system (such
> as WATBOX216 which is only for TIP3P).
The trick is that the atom names are the same for TIP3P and for POL3. So you
can use WATBOX216 to solvate the system, but load the POL3 force field
parameters....then you will get a pretty good starting point. The point is
this: WATBOX216 is not just for TIP3P. We should expand the manual to give
examples of the sort of thing you are trying.
(Do this on a small system first, so that you can manually check the prmtop
file to make sure you are getting what you want.)
>
> I tried stripping the atoms in ptraj using 'strip 1EP+', like 'strip :WAT',
> but this didn't work.
Try this syntax (untested!): "strip .EP+1"
You need the "." symbol to tell ptraj this is an atom; then you have to
realize that the internal name in Amber (look at the prmtop file, or use
the "desc" command in LEaP) is that given above. The "wrapping" of the final
"1" into the first column is a convention of PDB files, which have only four
total spaces for atom names, and some odd conventions about how names are to
be placed in there.
>
> 2. If one wants to put re/constraints on atoms in a system, such as
> cartesian constraints or a TMD restraint, should one include these extra
> point charges in the constrained group? For example, if one wants to put
> constraints on a backbone O atom, should one also apply a similar constraint
> to the 1EP+/1EP- charges associated with this atom, or are these point
> charges that mimic the lone-pair of electrons rigidly attached to their
> respective atom (such as in a united atom force-field)?
The extra points are rigidly connected to the "real" atoms of the system, and
their position is recalculated at each minimization or MD step, based on the
postions of the "real" atoms. So, nothing is gained by adding additional
constraints on them.
....hope you are having fun...sometime you should tell us what you are really
trying to do with these calculations.
....regards...dac
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Apr 05 2005 - 07:53:01 PDT
