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
> > _______________________________________________
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> > 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
> _______________________________________________
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Received on Mon Jan 24 2011 - 04:00:04 PST
