On Fri, Apr 29, 2011 at 4:34 PM, Samuel Genheden
<samuel.genheden.gmail.com>wrote:
> Hi, Jason
>
> The reason that ptraj as-far as I now cannot be used to create the
> truncated trajectories is because that we also keep water molecules in
> our buffer-region. The water molecules in the buffer region will
> constantly change, although there will roughly be the same number of
> water molecules there. What our program do is to extract the N nearest
> water molecules in each trajectory. I do not think this can be done
> easily with ptraj.
>
"closest" or "closestwater" does this. You could also feed a
distance-dependent amber mask.
>
> / Sam
>
> 2011/4/29 Jason Swails <jason.swails.gmail.com>:
> > On Fri, Apr 29, 2011 at 3:45 PM, Samuel Genheden
> > <samuel.genheden.gmail.com>wrote:
> >
> >> Hi
> >>
> >> I'm a PhD student with Ryde, so I felt that I should comment on this
> >> thread.
> >>
> >> We always use the perl script because the python script was not around
> >> when we started with our calculations, and we have seen no reason to
> >> change to the python script.
> >>
> >
> > It's probably easier to use for newcomers, and the input is
> namelist-style
> > like many other amber programs (and does a bit more out-of-the-box as of
> > AmberTools 1.5 than the perl script does), but your group has plenty of
> time
> > invested in understanding (and manipulating) the perl version that would
> > have to be redone if you switched -- not surprising that you haven't. I
> > still think the python version is a good place for newcomers to *start*,
> > since it's a bit easier to use (in that it catches user error and doesn't
> > require users to input what can be determined directly from the input
> files)
> > and actively supported on this list, but that doesn't apply to
> people/groups
> > with substantial investment in the perl version.
> >
> >
> >> We use nmode for the normal mode analysis, but as far as I understand
> >> this program is deprecated nowadays. We had to modify the nmode
> >> program so that we could use a belly in the calculations (i.e. a
> >> buffer region). These changes are described on our homepage:
> >> http://www.teokem.lu.se/~ulf/Methods/mm_pbsa.html
> >>
> >> Perhaps a similar change as to be done to the normal mode analysis
> >> code of nab, I'm not clear if nab allows you to keep something fixed
> >> in NMA.
> >>
> >
> > I don't think so, but I haven't looked at the nmode part of the nab code.
> > You can constrain stuff during minimizations (wcons), but I don't know
> how
> > (or if) this affects the normal mode calc. One nice thing that the nab
> code
> > has is the ability to include GB in the nmode calculation
> >
> >
> >> Also you need to have a special program to create the truncated
> >> trajectories for you. We have a program that goes through a
> >>
> >
> > Why? Will ptraj not work?
> >
> > trajectory, truncates it + a number of water molecules, and print a
> >> file for each snapshot. I'm sure that our program can be modified
> >> rather easily to get a single trajectory instead of many files.
> >>
> >
> > I'm pretty sure ptraj will do all of that with a simple "strip" command
> and
> > a trajout to the right format (PDB, restart with an appropriately paired
> > prmtop, etc.)
> >
> > All the best,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Apr 29 2011 - 08:00:05 PDT
