From: Johny Telecaster (johnytelecaster_at_gmail.com)
Date: Sat Nov 16 2013 - 10:46:01 CST
sorry,
I'm looking for script for calculation
2013/11/16 Johny Telecaster <johnytelecaster_at_gmail.com>
> Dear Munir,
>
> You investigations are very interesting. From your paper I've understood
> that to simulate unbinding is easily that binding (what you've actually do
> in your study) But your approach of multi-point MD might be still very
> useful.
>
>
> Little example
>
> -0.178 1.511 2.406 are the started coordinates corresponded to the COM of
> my ligand
>
> Supposing that I chose from the predicted dissociation path 4 extra
> points corresponded to the turn regions
>
> [-1.443, 2.706, 4.485],
> [0.180, 1.187, 9.484],
> [0.402, -2.330, 11.8940],
> [-0.127, -4.221, 17.162]
>
>
> Here you can see that 5 points (included starting points) are ranged
> mainly on Z (increasing Z from protein interior to the surrounding)
>
> No as I understtod 5 directions could not be defined in one conf file so I
> should to make 5 subsequent sMD simulations in each of which
>
> SMD on
> SMDFile smd_ref.pdb # corresponded to the ligand positioned in the
> initial COM xyz
> SMDk 5
> SMDVel .00001 ;# 10 A/ns = .01 A/ps = .00001 A/fs
> SMDDir -1.443, 2.706, 4.485 # corresponded to the 1rst point taken from
> the pathway
> SMDOutputFreq 100
>
> than the second conf should be
>
> SMD on
> SMDFile smd_ref2.pdb # should be taken as the output from the previous run
> SMDk 5
> SMDVel .00001 ;# 10 A/ns = .01 A/ps = .00001 A/fs
> SMDDir 0.180, 1.187, 9.484 # corresponded to the 2nd point taken from the
> pathway
> SMDOutputFreq 100
>
> etc (overall 5 simulations).
>
> Does such method correct in general ?
>
> My suggestion: I suppose that some problems might be arisen during the PMF
> calculations where ~10 windows extracted from the concatenated trajectory
> (from those 5 trajectories) will be needed. For example how I specify
> colvar precisely (typical its position restrictions on Z) for each window?
>
> Also could some one provide me with the script for analysis of the sMD
> data ( I'd like to measure force along time coordinate (not position as in
> the tutorial).
>
> Many thanks for suggestions,
>
>
> Johny
>
>
> 2013/11/16 Munir S. Skaf <skaf_at_iqm.unicamp.br>
>
>
>> Dear Johny,
>>
>> Perhaps you don't need to define your SMD routes precisely along a cuved
>> path, but it may
>> turn out that a few (say, 3 or 4) turning points on a given pathway are
>> sufficient to smoothly
>> drive your ligand out of the enzyme.
>> You have to make educated guesses to define the turning points.
>> Please take a look at Leandro Martínez's work:
>>
>> J. Phys. Chem. B 2008, 112, 10741–10751
>> This multi-point SMD approach preserves the desired physics of the
>> force profile.
>> Best,
>> munir
>>
>>
>>
>> On Sat, Nov 16, 2013 at 9:10 AM, Johny Telecaster <
>> johnytelecaster_at_gmail.com> wrote:
>>
>>> Dear NAMD Developers,
>>>
>>>
>>> I have some questions about stereed MD. In particular I'd like to
>>> simulate ligand unbinding from the enzyme. Using CAVER Pymol plugin I've
>>> detected 3 possible paths inside my protein. Now I'd like to run stereed MD
>>> along each of that routes to measure forces affected on the ligand during
>>> its motions along each of it. How I could define force directions
>>> presicely along CAVER paths? Does it possible to define this pathes as the
>>> colvar restrictions? Please provide me with example.
>>>
>>>
>>> Many thanks for the suggestions,
>>>
>>>
>>> Johny T.
>>> Scanned and tagged with DSPAM 3.10.2 by Instituto de Quimica - Unicamp
>>> !DSPAM:106,5287537b107521489016123!
>>
>>
>>
>>
>> --
>> Munir S. Skaf
>> Institute of Chemistry - Cx. P. 6154
>> State University of Campinas - UNICAMP
>> Campinas - SP 13084-862, Brazil
>> Tel. 55 19 3521 3093 / Fax: 3521 3023
>>
>
>
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