Would do and update.
Thanks
Sent from Mail<
https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
From: Carlos Simmerling<mailto:carlos.simmerling.gmail.com>
Sent: 31 October 2020 08:43
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] NMR restraints
then check Dave Case's suggestion
On Sat, Oct 31, 2020 at 8:41 AM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:
> 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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> >
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Received on Sat Oct 31 2020 - 06:00:03 PDT
