Re: [AMBER] Restraint removal doesn't seem to be happening

From: David A Case <>
Date: Fri, 14 Jan 2022 21:55:11 -0500

On Fri, Jan 14, 2022, Daniel Burns wrote:
> &cntrl
> imin=0, irest=1, ntx=5, iwrap=1,
> nstlim=15000000, dt=0.002,
> ntc=2, ntf=2,
> cut=10.0, ntb=2, ntp=1, taup=1.0,
> ntpr=2000, ntwx=2000, ntwr= 2000,
> ntt=3, gamma_ln=2.0, temp0=303.15,
> ntr = 1, restraintmask =":479<:5&!.H=",
> restraint_wt = 1.0, nmropt=1,
> &end
> &wt type='REST', istep1=0, istep2=10000000, value1=1.0, value2=0.0, &end
> &wt type='REST', istep1=10000001, istep2=15000000, value1=0.0, value2=0.0, &end
> &wt type='END' &end

Oh, my. It may be that the REST in the &wt namelist doesn't mean what you
think it does. These refer to "NMR restraints"
(bonds/angles/torsions/etc.). But you don't appear to have defined any such

The "restraint_wt" and "restraintmask" refer to Cartesian restraints that
keep the atoms near to their positions in the reference structure. There is
no way to have restraint_wt depend upon step number.

I can see how easy it would be to confuse two things that have such similar
names. At a minimum, we need to add an explicit warning to the manual.
Changing "restraint_wt" to something like coordinate_restraint_wt" would
help, but would have a big backwards-incompatibility downside. Volunteers
are solicited to pitch in to make this better.


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Received on Fri Jan 14 2022 - 19:00:02 PST
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