you still have nmropt=1 and restraintmask=':1-242', so you don't just have
dihedral restraints. try setting nmropt=1 to see if that reduces the large
restraint penalty. from there you'll want to decide which one you use (they
can be combined, with caution)
On Fri, Mar 8, 2024 at 5:21 PM Kari Gaalswyk via AMBER <amber.ambermd.org>
wrote:
> Hi,
>
> Thanks for the tips, those solved that problem (it was an issue with the
> number of spaces). I'm still running into some trouble however regarding
> the restraints themselves. I am able to minimize the system using the
> following scripts (we typically do a 2 stage minimization):
>
> min1:
> energy minimization stage 1
> &cntrl
> imin=1, maxcyc=50000, ncyc=25000,
> cut=9.0, ntb=1,
> ntc=1, ntf=1,
> ntpr=10,
> ntr=1, nmropt=1,
> restraintmask=':1-242',
> restraint_wt=10.0
> /
> &wt type='END'/
> DISANG=RST
>
> min2:
> energy minimization stage 2
> &cntrl
> imin=1, maxcyc=100000, ncyc=50000,
> cut=9.0, ntb=1,
> ntc=1, ntf=1, nmropt=1
> ntpr=10,
> /
> &wt type='END'/
> DISANG=RST
>
> When it comes time for heating, it fails on the first step with the
> following error:
> Error: an illegal memory access was encountered launching kernel
> kClearForces.
>
> And the .out file looks like this:
>
> --------------------------------------------------------------------------------
> 4. RESULTS
>
> --------------------------------------------------------------------------------
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> 0.0
> Etot = -177544.3812 EKtot = 0.0000 EPtot =
> -177544.3812
> BOND = 142.4921 ANGLE = 661.5008 DIHED =
> 1153.3724
> UB = 0.0000 IMP = 0.0000 CMAP =
> 179.2879
> 1-4 NB = 745.0276 1-4 EEL = 10619.5497 VDWAALS =
> 35317.3582
> EELEC = -229311.6288 EHBOND = 0.0000 RESTRAINT =
> 2948.6590
> EAMBER (non-restraint) = -180493.0402
>
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 2948.659
>
> ===============================================================================
>
> The heating script is:
> heating
> &cntrl
> imin=0,irest=0,ntx=1,
> nstlim=500000,dt=0.002,
> ntc=2,ntf=2, nmropt=1,
> cut=9.0, ntb=1,
> ntpr=500, ntwx=500,
> ntt=3, gamma_ln=2.0, ig=-1,
> tempi=0.0, temp0=300.0,
> ntr=1, restraintmask=':1-242',
> restraint_wt=1.0, nmropt=1
> /
> &wt TYPE='TEMP0', istep1=0, istep2=500000,
> value1=0.1, value2=300.0, /
> &wt TYPE='END' /
> DISANG=RST
>
> The torsional restraints are defined based on the initial structure (using
> the rst command from cpptraj) with the following format:
>
> &rst iat=39,41,42,48,0
> r1=-81.942178, r2=-61.942178, r3=-61.942178, r4=-41.942178,
> rk2=10.000000, rk3=10.000000,
> nstep1=0, nstep2=0,
> &end
> &rst iat=41,42,48,50,0
> r1=-55.201449, r2=-35.201449, r3=-35.201449, r4=-15.201449,
> rk2=10.000000, rk3=10.000000,
> nstep1=0, nstep2=0,
> &end
>
> I'm more familiar with distance restraints, but I'd assume a 10-degree
> separation between r1-r2 and r3-r4 would be sufficient, and the force
> constant doesn't seem large, although the energies seem to disagree. To
> clarify, there are only torsional restraints for this system. Any hints
> would be appreciated.
>
> Thank you,
> Kari Gaalswyk
> University of Denver
> ________________________________
> From: David A Case <dacase1.gmail.com>
> Sent: Wednesday, January 17, 2024 9:50 AM
> To: Kari Gaalswyk <Kari.Gaalswyk.du.edu>; AMBER Mailing List <
> amber.ambermd.org>
> Subject: [EXTERNAL] Re: [AMBER] No restraint defined when using torsional
> restraints
>
> [External Email From]: dacase1.gmail.com
>
> On Mon, Jan 15, 2024, Kari Gaalswyk via AMBER wrote:
> >
> >I am trying to apply torsion restraints throughout the system, and the
> >restraints are not being recognized during the minimization phase. I used
> >makeANG_dist to create the RST file, and the min.in file is below:
> >
> > Restraints will be read from file: RST
> >Here are comments from the DISANG input file:
> >
> > ** No restraint defined **
> >
> > Done reading weight changes/NMR restraints
> >
> >The RST file looks like this:
> >
> >&rst iat = 34,36,37,43,
> >r1 = -100.0, r2 = -80.00000, r3 = -40.00000, r4 = -20.0,
> >rk2 = 10, rk3 = 10,
> >&end
> >
> >&rst iat = 36,37,43,45,
> >r1 = -100.0, r2 = -80.00000, r3 = -40.00000, r4 = -20.0,
> >rk2 = 10, rk3 = 10,
> >&end
>
> A few ideas that *might* help:
>
> 1. The use of "&end" to end a namelist input is way outdated. Try using
> "/"
> instead. (Most compilers still accept "&end", but some might not.)
>
> 2. Namelist list originally required a space in column 1. Like point 1
> above, most compilers will not enforce this, but it's worth a try.
>
> 3. Add "LISTIN=POUT" to you directives. This will print out details about
> how the code is interpreting your restraints. But it looks like no
> restraints are being read. Fiddle with the input file in various ways to
> see if you can figure out why. Compare carefully the RST file you used
> earlier in a "similar" calculation -- that might help.
>
> ...good luck...dac
>
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>
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Received on Fri Mar 08 2024 - 15:00:02 PST
