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.
/ 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
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 29 2011 - 08:00:06 PDT
