I guess it would work roughly as you say
1.) Create a prmtop for the "core" region
2.) Minimize the core+buffer region with buffer region fixed
3.) Cut away the buffer region
4.) Calculate NMA on core region
2011/4/29 Jason Swails <jason.swails.gmail.com>:
> 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
>> >> > _______________________________________________
>> >> > 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
>>
>
>
>
> --
> 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 - 08:30:03 PDT
