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 Tue Apr 12 2011 - 07:00:03 PDT
