Re: [AMBER] NMR restraints not responding to 'value' flags in AMBER16 (pmemd.cuda)

From: ankita mehta <>
Date: Sat, 23 Jul 2016 13:39:16 +0530

Value of rk2 and rk3 is the value of force constants actually and if u make
them zero that means no force and ligand runs away.what u can do is in
subsequent runs take the value of rk3 to lower and lower.this way ur ligand
will no longer run at reduced value.
Value of rk2 is set to certain base value ..u can see the manual.i think it
is 20.
I guess this is the solution.

On Jul 23, 2016 4:31 AM, "Wesley Michael Botello-Smith" <>

> Hello all,
> I am running a simulation under AMBER16 using pmemd.cuda. I am attempting
> to use NMR restraints to hold a ligand in place during equilibration, then
> gradually release the restraints in preparation for production run.
> To accomplish this, I am using 'nmropt=1' under the '&cntrl' list and
> afterward:
> &wt type='REST', istep1=1,istep2=200000,
> value1=1.0,value2=0.0, !ramp down restraint to 0
> &end
> &wt type='DUMPFREQ', istep1=1000,
> &end
> &wt type='END',
> &end
> DUMPAVE=step4.4_equilibration.distout
> The nmr restraint file ( reads:
> &rst
> ixpk= 0, nxpk= 0, iat=1276, 7908, r1=0.0, r2=2.0, r3=2.0, r4=4.0,
> rk2=50.0, rk3=50.0, ir6=0, ialtd=0,
> &end
> Upon examination of the resulting trajectory, amber output and distout
> files, I see that the distance between the two restrained atoms remains
> roughly constant at about 2.8 to 3.0 Å
> If, however, I set rk2=0.0 and rk3=0.0, the restrained atoms move away
> rapidly from their starting postion at about 2.9 to a distance of about 4.5
> over the 200ps trajectory.
> Is this a bug or am I doing something wrong in my setup?
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Received on Sat Jul 23 2016 - 01:30:02 PDT
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