On Thu, Nov 06, 2008 at 04:48:47PM -0600, Jianyin Shao wrote:
> Hi, Bud,
>
>
> When you select atoms based on distance criteria in ptraj, you need to
> provide the atom coordinates for ptraj using a "reference ref.cor" command
> before other ptraj commands. Due to the reason that the ptraj determines the
> atom masks at the beginning of the processing, the atom selection is not
> dynamic. The rdparm cannot take "reference" as a command, so please chek
> your ptraj output to make sure the atom masks are correctly selected.
>
> Best,
>
> Jianyin Shao
>
OK! Thanks. That is easy enough to satisfy. I'll try it tomorrow.
Bud
PS, I had already figured out that rdparm, having only the prmtop file
when I issued the checkmask command, could not have done distances.
PPS, thinking about this some more, your answer would seem to imply
that the identities of the waters selected by distance would be fixed
by the reference coordinates. That does not work very well for my
purpose, since I wanted to see the waters come and go into and out of
the region of the active site over the trajectory. Is this correct?
Does anyone know if vmd can do active selections of this type across a
trajectory? (Eventually, I want to make a movie.)
> On Thu, Nov 6, 2008 at 12:31 PM, M. L. Dodson <
> activesitedynamics.comcast.net> wrote:
>
> > Hi folks,
> >
> > I was trying to recover a pdb of active site residues and close waters
> > (using ptraj from AmberTools1.2) with the following command:
> > strip "!((:1,22,144,145) | (.2478 <:4.2 & :WAT))"
> >
> > This works fine in ambmask when checked without the negating !() to
> > keep the size down. I.e, ambmask should give the identify of the
> > residues left after the ptraj strip command, and ambmask does identify
> > the desired residues. However, ptraj drops core and gives a nonsense
> > pdb file (includes a bunch of seemingly random solute and water
> > atoms). Checkmask in rdparm just drops core with a segmentation fault
> > after printing a whole bunch of atom strings either with or without
> > the negating !().
> >
> > Is anything obviously wrong with this? Has this behavior been
> > documented?
> >
> > I tried the search engine on the archive, but may have failed due to
> > lack of search string foo.
> >
> > Bud Dodson
> >
> > PS,
> > strip "!(:1,22,144,145)"
> > works fine
> > strip "!(.2478 <:4.2 & :WAT)"
> > behaves the same as the whole strip mask given above.
> > --
> > M. L. Dodson
> > Business Email: activesitedynamics-at-comcast-dot-net
> > Personal Email: mldodson-at-comcast-dot-net
> > Phone: eight_three_two-56_three-386_one
> > -----------------------------------------------------------------------
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> >
--
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email: mldodson-at-comcast-dot-net
Phone: eight_three_two-56_three-386_one
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Received on Fri Dec 05 2008 - 11:09:07 PST
