Restraining both protein and ligand during the equilibration
guarantees that protein-ligand interactions that take place in initial
system will not be lost.
So I believe it is a good way.
On Mon, Jan 24, 2011 at 2:39 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com> wrote:
> Thank You Sunita,
> It runs fine.. Just one query.. For my complex (i.e. protein bound to two
> ligand) Do I need to* restrain the protein only* or the* protein as well as
> both the ligands* as well during heating??
>
> Please give me your suggestion for the same?
>
> Thanks
> Hirdesh
>
> On Mon, Jan 24, 2011 at 2:56 PM, sunita gupta <sunita.bio.gmail.com> wrote:
>
>> You can also use this file for slow heating...also, when you use
>> restraints
>> ie. ntr =1, a reference coordinate is required as input...(-ref flag)..use
>> the same you are using with -c
>> Heating the system linearly with weak restraints
>> &cntrl
>> imin = 0,
>> irest = 0,
>> ntx = 1,
>> ntb = 1,
>> cut = 12,
>> ntr = 1,
>> ntc = 2,
>> ntf = 2,
>> tempi = 0.0,
>> temp0 = 300.0,
>> ntt = 3,
>> gamma_ln = 1.0, nmropt=1,
>> nstlim = 50000, dt = 0.002
>> ntpr = 100, ntwx = 100, ntwr = 1000
>> /
>> &wt TYPE='TEMP0', istep1=0, istep2=40000,
>> value1=0.1, value2=300.0, /
>> &wt TYPE='DUMPFREQ',ISTEP1=10, /
>> &wt TYPE='END' /
>> Keep protein fixed
>> 5.0
>> RES 1 92
>> END
>> END
>>
>> Hope this helps you
>>
>> On Mon, Jan 24, 2011 at 12:45 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com
>> >wrote:
>>
>> > Hi All,
>> > I am trying gradually heat my system from 0K to 300K. When i put no
>> > restrain
>> > then it runs fine, but in case of restrain, it is showing some error.
>> > Below mentioned is my mdin file:
>> > Heating up the system equilibration stage 1
>> > &cntrl
>> > imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10.0, ntr
>> > = 1, ntc = 2, ntf = 2,
>> > ig = 209833, tempi = 0.0, temp0 = 300.0, ntt = 3, gamma_ln
>> =
>> > 1.0, nstlim = 300000, dt = 0.002,
>> > ntpr = 1, ntwx = 100, ntwr = 1000, nmropt=1
>> > /
>> > &wt
>> > type='TEMP0', istep1=0, istep2=20000, value1=0, value2=20,
>> > /
>> > &wt
>> > type='TEMP0', istep1=20001, istep2=40000, value1=20, value2=40,
>> > /
>> > &wt
>> > type='TEMP0', istep1=40001, istep2=60000, value1=40, value2=60,
>> > /
>> > &wt
>> > type='TEMP0', istep1=60001, istep2=80000, value1=60, value2=80,
>> > /
>> > &wt
>> > type='TEMP0', istep1=80001, istep2=100000, value1=80, value2=100,
>> > /
>> > &wt
>> > type='TEMP0', istep1=100001, istep2=120000, value1=100, value2=120,
>> > /
>> > &wt
>> > type='TEMP0', istep1=120001, istep2=140000, value1=120, value2=140,
>> > /
>> > &wt
>> > type='TEMP0', istep1=140001, istep2=160001, value1=140, value2=160,
>> > /
>> > &wt
>> > type='TEMP0', istep1=160001, istep2=180001, value1=160, value2=180,
>> > /
>> > &wt
>> > type='TEMP0', istep1=180001, istep2=200000, value1=180, value2=200,
>> > /
>> > &wt
>> > type='TEMP0', istep1=200001, istep2=220001, value1=200, value2=220,
>> > /
>> > &wt
>> > type='TEMP0', istep1=220001, istep2=240000, value1=220, value2=240,
>> > /
>> > &wt
>> > type='TEMP0', istep1=240001, istep2=260001, value1=240, value2=260,
>> > /
>> > &wt
>> > type='TEMP0', istep1=260001, istep2=280000, value1=260, value2=280,
>> > /
>> > &wt
>> > type='TEMP0', istep1=280001, istep2=300000, value1=280, value2=300,
>> > /
>> > &wt
>> > type='END'
>> > /
>> > Keep Protein fixed with weak restraints
>> > 10.0
>> > RES 1 336
>> > END
>> > END
>> >
>> >
>> > The error which I am getting in output file is:
>> >
>> >
>> > ----- READING GROUP 1; TITLE:
>> > Keep Protein fixed with weak restraints
>> >
>> >
>> > GROUP 1 HAS HARMONIC CONSTRAINTS 10.00000
>> > GRP 1 RES 1 TO 336
>> > Number of atoms in this group = 5326
>> > ----- READING GROUP 2; TITLE:
>> > END
>> >
>> >
>> > rfree: End of file on unit 5
>> >
>> >
>> > Please suggest me where I am wrong..
>> >
>> > Thanks,
>> > Hirdesh
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> --
>> SUNITA GUPTA
>> Member Research Staff
>> LeadInvent Technologies Pvt.Ltd
>> Biotech Centre, University of Delhi
>> South Campus, Benito Juarez Road,
>> New Delhi, Pin 110021
>> Email- sunita.leadinvent.com
>> _______________________________________________
>> AMBER mailing list
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>>
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Dmitry Nilov,
Lomonosov Moscow State University
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Received on Mon Jan 24 2011 - 04:00:07 PST
