Dear Carlos,
Thank you for the suggestions. TMD was done with considerable amount of
equilibration and for 10ns. And yes, the final structures have reached a
rmsd of 0.558A. Trajectories look good and as expected. And, for NEB the
final(close form) and initial(open form) crystal structures are
available.
Thank you,
Aravind R
National Center for Biological sciences
Bangalore, India
> Your plan sounds reasonable, depending on the structures that you obtained
> from the TMD. Did you look at the outputs? Do you actually achieve low
> rmsd
> at the end? That can be challenging. NEB depends strongly on the endpoint
> structures, so if you feel those are good representation then go ahead
> with
> NEB.
>
> On Fri, Apr 20, 2018, 5:33 AM Aravind Ravichandran <raravind.ibab.ac.in>
> wrote:
>
>> Dear Amber Users/Authors,
>> I am intending to perform NEB simulations for finding low energy
>> pathways
>> for transition between an open and close form of a protein. I have
>> already
>> performed TMD simulation from open to close form.
>>
>> Now, can I generate multiple snapshots along the TMD trajectory and use
>> it
>> as an input for simulated annealing and NEB, after a thorough
>> minimization
>> on the
>> structures??
>> Or is it better to do generate replicas by heating, as mentioned in the
>> manual so that the process is random and not biased??
>> Will results differ in both the cases??
>>
>> This is how I ran my TMD simulation(10ns, with equilibration in
>> between).
>>
>> Ubi targeted MD
>> &cntrl
>> imin = 0, nstlim = 5000000, dt = 0.002,
>> ntx = 1, ntt = 3, gamma_ln = 1.0,
>> ntc = 2, ntf = 2, ntb = 2, ntp=1,
>> cut = 10.0, nscm = 0,
>> ntpr = 1000, ntwx = 1000, ntwr = 1000,
>> igb = 0, irest=0, nmropt=1,tempi=300.0,
>> itgtmd=1, tgtmdfrc=0.25,
>> tgtfitmask=":77-222.CA,N,C,O",
>> tgtrmsmask=":1-70.CA,N,C,O",
>> /
>> &wt
>> TYPE='TGTRMSD', istep1 =0, istep2 = 400000,
>> value1 = 40.957, value2 = 35.0,
>> /
>> &wt
>> TYPE='TGTRMSD', istep1 =400001, istep2 = 600000,
>> value1 = 35.0, value2 = 35.0,
>> /
>> &wt
>> TYPE='TGTRMSD', istep1 =600001, istep2 = 1000000,
>> value1 = 35.0, value2 = 30.0,
>> /
>> &wt
>> TYPE='TGTRMSD', istep1 =1000001, istep2 = 1200000,
>> value1 = 30.0, value2 = 30.0,Any help is appreciated and thanks in
>> advance!!
>>
>> ---------------------------------------------------------
>> Aravind R
>> National Center for biological sciences
>> Banglore, India
>> /
>> &wt
>> TYPE='TGTRMSD', istep1 =1200001, istep2 = 1600000,
>> value1 = 30.0, value2 = 25.0,
>> /
>> &wt
>> TYPE='TGTRMSD', istep1 =1600001, istep2 = 1800000,
>> value1 = 25.0, value2 = 25.0,
>> /
>> &wt
>> TYPE='TGTRMSD', istep1 =1800001, istep2 = 2200000,
>> value1 = 25.0, value2 = 20.0,
>> /
>> &wt
>> TYPE='TGTRMSD', istep1 =2200001, istep2 = 2400000,
>> value1 = 20.0, value2 = 20.0,
>> /
>> &wt
>> TYPE='TGTRMSD', istep1 =2400001, istep2 = 2800000,
>> value1 = 20.0, value2 = 15.0,
>> /
>> &wt
>> TYPE='TGTRMSD', istep1 =2800001, istep2 = 3000000,
>> value1 = 15.0, value2 = 15.0,
>> /
>> &wt
>> TYPE='TGTRMSD', istep1 =3000001, istep2 = 3400000,
>> value1 = 15.0, value2 = 10.0,
>> /
>> &wt
>> TYPE='TGTRMSD', istep1 =3400001, istep
>>
>> Any help is appreciated and thanks in advance!!
>>
>> ---------------------------------------------------------
>> Aravind R
>> National Center for biological sciences
>> Bangalore, India
>>
>>
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Received on Sat Apr 21 2018 - 02:30:02 PDT
