Samuel,
I'm going to contact you during next week. Besides the entropy issue, I
would like to describe my study (that is very much inspired from your work:
How to get converged MMPBSA results 2009) and you are invited to give some
++ on what you would find worth to investigate on my accumulated simulation
data.
Cheers,
Olli
Am 29.04.2011 16:34 schrieb "Samuel Genheden" <samuel.genheden.gmail.com>:
> 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 - 08:00:07 PDT
