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.
/ 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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Received on Fri Apr 29 2011 - 08:00:04 PDT
