Hi Matthias,
you are free to set these as you wish, just as you suggest. You might
fix part of the protein in space, and map the path for another set of
atoms moving relative to the first.
we'll work on getting more tutorials for these, but as always finding
time to write tutorials can be a challenge.
carlos
On Tue, Apr 12, 2011 at 9:31 AM, Matthias Negri
<m.negri.mx.uni-saarland.de> wrote:
> Hi,
> first of all, this subject is very interesting for us and it might be of
> general interest (perhaps) to get a broader tutorial, not only focusing
> on small molecules.
>
> Then, here comes my question:
> I read through the journal referenced as well as the tutorial, but I
> still have some doubts concerning the usage of tgtfitmask and tgtrmsmask
> in NEB. As far I have understood in multiple MD these can be different,
> which might be helpfull when only parts of the proteins are going to be
> considered. To bring a direct example, I'd tried
> tgtfitmask=":1-207,214-536,543-658.CA,N,C,O,H,HA" (the protein part
> which should not move) and tgtrmsmask=":208-213.CA,N,C,O" (the changing
> part of the protein, expected to move along according to the given RMS
> value) to simulate the progression from state A to state B.
> Might I also apply this criteria to NEB or do I need to choose the same
> range of residues, eventually using different atom types (on which to
> apply the NEB force, as in the NEB tutorial)?
>
> Best regards,
>
> Matthias
>> the NEB option in sander is probably the best Amber option for this.
>> You could also run targeted MD, starting with one structure and using
>> the RMSD restraint to force it to the other, but that can give high
>> forces at the start and tends to give direct paths that may not be
>> optimal.
>>
>> If you go with NEB, use the Amber11 version. A tutorial and journal
>> reference for our NEB version can be found at
>> http://ambermd.org/tutorials/advanced/tutorial5_amber11/
>>
>>
>> On Tue, Apr 12, 2011 at 7:43 AM, Bernhard Poll
>> <poll.chemie.uni-hamburg.de> wrote:
>>> Hi Amber users,
>>>
>>>
>>>
>>> I've got some questition about MD's. Is it possible to define some start and
>>> end structure (and may be a transition state) of a protein in Amber and run
>>> a MD simulation? We know these points from crystal analysis and we're just
>>> wondering if it is possible to run the transition so we can understand this
>>> behavior.
>>>
>>>
>>>
>>> Thanks in advance
>>>
>>>
>>>
>>> Bernhard
>>>
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Received on Thu Apr 14 2011 - 12:00:03 PDT
