Hello Prof Simmerling,
Really appreciate your feedback on this.
Yes, NMR Bond Angle and Torsion stay 0 throughout all steps of my minimization.
Thanks
Debarati
From: Carlos Simmerling<mailto:carlos.simmerling.gmail.com>
Sent: 30 October 2020 17:12
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] NMR restraints
if it's step 1 this may just mean that your input structure satisfies the
restraints. does is stay 0 at later steps?
On Fri, Oct 30, 2020 at 3:38 PM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:
> Hi All
> I was trying to set up a minimization (TI run) and I see that NMR bond
> angle Torsion energies are all 0.
> Is there something wrong with my format?
> Thanks
> Debarati
>
>
>
>
> This is my input file:
> Minimization:-
> &cntrl
> imin = 1, ntmin = 2,
> maxcyc=80000,
> ntpr = 100, ntwe = 100, ntwx =100, ntwv=-1,
> ntave=100,
> iwrap = 1,
> nsnb = 10,
> ntb = 1,
> ioutfm=1,
> icfe = 1, ifsc = 1, clambda=0.43738, scalpha = 0.5, scbeta = 12.0,
> timask1=':IPA', scmask1=':IPA',
> timask2='', scmask2='',
> nmropt=1,
> /
> &wt type='DUMPFREQ', istep1=1, /
> &wt type='END', /
> DISANG=output.disang
> DUMPAVE=dist_0.43738.dat
> LISTIN=POUT
> LISTOUT=POUT
>
>
>
>
>
>
> | Nonbonded Pairs Initial Allocation: 476900
>
> | Running AMBER/MPI version on 24 MPI task
>
>
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
> ---------------------------------------------------
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
> ---------------------------------------------------
> |---------------------------------------------------
> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
> | with 50.0 points per unit in tabled values
> | Relative Error Limit not exceeded for r .gt. 2.47
> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
> | with 50.0 points per unit in tabled values
> | Relative Error Limit not exceeded for r .gt. 2.89
> |---------------------------------------------------
>
> | TI region 1
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -1.3675E+05 1.3020E+01 1.0903E+02 CG 4107
>
> BOND = 848.4796 ANGLE = 2244.8532 DIHED =
> 3441.8034
> VDWAALS = 13187.2043 EEL = -168584.6849 HBOND =
> 0.0000
> 1-4 VDW = 1003.6064 1-4 EEL = 11112.8711 RESTRAINT =
> 0.0000
> DV/DL = 16.3147
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
> Softcore part of the system: 12 atoms, TEMP(K) =
> 0.00
> SC_Etot= 0.0000 SC_EKtot= 0.0000 SC_EPtot =
> -13.4015
> SC_BOND= 2.1641 SC_ANGLE= 3.7362 SC_DIHED =
> 0.4361
> SC_14NB= 0.6468 SC_14EEL= -39.3219 SC_VDW =
> -0.0681
> SC_EEL = 19.0054
> SC_RES_DIST= 1.3596 SC_RES_ANG= 0.0000 SC_RES_TORS=
> 0.0000
> SC_EEL_DER= 0.4854 SC_VDW_DER= -0.5845 SC_DERIV =
> -0.0992
>
> ------------------------------------------------------------------------------
>
>
> | TI region 2
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -1.3675E+05 1.3020E+01 1.0903E+02 CG 4107
>
> BOND = 848.4796 ANGLE = 2244.8532 DIHED =
> 3441.8034
> VDWAALS = 13187.2043 EEL = -168584.6849 HBOND =
> 0.0000
> 1-4 VDW = 1003.6064 1-4 EEL = 11112.8711 RESTRAINT =
> 0.0000
> DV/DL = 16.3147
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
> ===============================================================================
>
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Received on Sat Oct 31 2020 - 06:00:02 PDT
