On Fri, Apr 29, 2011 at 4:47 PM, Samuel Genheden
<samuel.genheden.gmail.com>wrote:
> Great, I was not aware of that.
>
> The problem is still in the nab-code,
> I cannot see that you can specify not to include certain atoms in NMA.
> Perhaps there is some roundabout way.
>
What about just stripping those atoms out via ptraj and dumping a PDB, and
loading that PDB into nab? (There's still the issue of needing a matching
prmtop, but that's pretty easy)...
> / Sam
>
> 2011/4/29 Jason Swails <jason.swails.gmail.com>:
> > 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
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> >> > 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
> > _______________________________________________
> > 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 - 08:00:09 PDT
