Hey Bhara,
Don't get confused. Restraintmask is used when a certain stretch needs
to be fixed at its own coordinates and everything else is kept under
motion.
ibelly=1 with bellymask is just opposite, where the selected portion just moves.
As per your query ntr=1 is mostly employed when you need to minimize a
system, which is explicitly solvated, and you just want to correct the
orientation and coordinate system of solvent residues, keeping your
protein confirmation fixed. In this case the whole system is minimized
energetically after this step.
Now i guess you are clear with it.
Regards
Ashish Runthala
On Sat, Aug 1, 2009 at 5:37 PM, bharat lakhani<lakhbharat.gmail.com> wrote:
> I want to know that what is the exact logic behind restrainedmask
> syntax can i get some useful tutorial on this so that i can use it in
> more logical way.
> thanks
> Bharat
>
> On Fri, Jul 31, 2009 at 1:12 PM, bharat lakhani<lakhbharat.gmail.com> wrote:
>> Sir / Madam,
>>
>> During minimization if i want to fix the secondary structure part
>> (alpha helix) and move rest of the part is it possible to do it ?
>> I mean a type of constrained minimization where internal
>> parameters(bond angle,bond length,backbone torsion angle) of helix is
>> fixed its behaving as one big molecule. So it is moving as one
>> molecule from one place to another without disturbing the helix
>> structure.
>>
>> Can you please tell me the process to carry these things.
>>
>> Thanks
>> Bharat
>>
>
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--
Ashish Runthala,
Faculty Division III,
Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA
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Received on Wed Aug 19 2009 - 20:03:26 PDT
