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.
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.
Also you need to have a special program to create the truncated
trajectories for you. We have a program that goes through a
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 had in mind to implement it in nab, but I haven't got around to it.
I guess we could discuss by regular e-mail how to proceed.
Best regards,
Samuel Genheden
University of Lund
2011/4/29 Jason Swails <jason.swails.gmail.com>:
> But the minimization is done with nab now -- there is no input file. You actually have to modify the nab program mmpbsa_entropy.nab. See the AmberTools manual --especially the wcons variable -- for addin restraints.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On Apr 28, 2011, at 12:10 PM, Oliver Kuhn <oak.amber.googlemail.com> wrote:
>
>> Ok. I'm sure I get along somehow without the perl version since I just have
>> to modify the input for the minimization step.
>>
>> Cheers,
>> Olli
>> Am 28.04.2011 17:59 schrieb "Jason Swails" <jason.swails.gmail.com>:
>>>
>>> I think I'd tend to agree with Markus on this one (although Ryde's MM/PBSA
>>> papers use the perl version). I'm not sure how you would go about
>>> accomplishing the buffer region in the nab program, and I'm pretty sure
>> Ryde
>>> et. al. used the nmode program as well.
>>>
>>> All the best,
>>> Jason
>>>
>>> On Thu, Apr 28, 2011 at 6:18 AM, Oliver Kuhn <oak.amber.googlemail.com
>>> wrote:
>>>
>>>> Again, Jason,
>>>>
>>>> I can remember I have asked something similar few month (or maybe a year
>> ;)
>>>> ago.
>>>> I would like to use the method from:
>>>> An improved method to predict the entropy term within the MMPBSA
>> approach,
>>>> Kongsted Ryde, J Comput Aided Mol Des 2009
>>>>
>>>> The main reason is that it will be more computationally efficient and
>> I'm
>>>> interested how the distribution of entropy estimates will be compared to
>>>> usual NMA.
>>>>
>>>> The method minimizes a truncated 8A environment around the ligand but
>> with
>>>> a
>>>> 4A fixed buffer region.
>>>> Thus, I would tend to input a traj with the 12A environmental residues
>>>> around the ligand to the NMA routine in the MMPBSA.py script.
>>>> Can you suggest an easy way to tell the script to keep the 4A buffer
>> region
>>>> fixed during minimization - in other words, where do I have to change
>> the
>>>> code and set restraints?
>>>>
>>>> And b.t.w. thanks also to Bill and Carlo for the discussion on the usage
>> of
>>>> internal dielectric 1,2,4.
>>>>
>>>> Regards,
>>>> Oliver
>>>>
>>>> --
>>>> Oliver Kuhn, Department of Bioinformatics,
>>>> Center for Medical Biotechnology, University of Duisburg-Essen,
>>>> Universitätsstr. 1-5, 45141 Essen, Germany
>>>> phone +49 201 183-3121, oliver.kuhn.uni-due.de
>>>> _______________________________________________
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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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Received on Fri Apr 29 2011 - 07:00:02 PDT
