Thank you David, that worked. I used the following input:
Run NVT simulation at 298 K
&cntrl
imin = 0, ntx = 1, irest = 0,
ntpr = 500, ntave = 5000,
ntwr = 500,
ntwx = 100, ntwe = 0,
ntf = 2, ntc = 2, ntb = 1,
cut = 12.0, nsnb = 10,
nstlim = 1000000, dt = 0.001,
tempi = 0, temp0 = 298.0,
ntt = 3, tautp = 1.0,
ig=-1, ifqnt=1, nmropt = 1,
/
&qmmm
qmmask = ':2967',
qmcharge = -1,
qm_theory = 'DFTB3',
qmshake = 0, diag_routine = 0,
qm_ewald = 1, qm_pme = 1,
printcharges = 1, printdipole = 1, verbosity = 0
/
&wt type='END'
/
DISANG=dist.RST
And sander is able to correctly read the given the restraints, as seen below:
RESTRAINTS:
Requested file redirections:
DISANG = dist.RST
Restraints will be read from file: dist.RST
Here are comments from the DISANG input file:
Number of restraints read = 2
Done reading weight changes/NMR restraints
-----Original Message-----
From: David A Case <david.case.rutgers.edu>
Sent: Thursday, April 20, 2023 9:06 AM
To: Abdullah Bin Faheem <Abdullahbinfaheem.hotmail.com>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Restraints not read by Sander for QM/MM
On Wed, Apr 19, 2023, Abdullah Bin Faheem via AMBER wrote:
>
>Run NVT simulation at 298 K
>&cntrl
> imin = 0, ntx = 1, irest = 0,
> ntpr = 500, ntave = 5000,
> ntwr = 500,
> ntwx = 100, ntwe = 0,
> ntf = 2, ntc = 2, ntb = 1,
> cut = 12.0, nsnb = 10,
> nstlim = 1000000, dt = 0.001,
> tempi = 298, temp0 = 298.0,
> ntt = 3, tautp = 1.0,
> ig=-1, ifqnt=1, nmropt = 1,
>/
>&wt type='DUMPFREQ', istep1=100
>/
>&wt type='END'
>/
>&qmmm
> qmmask = ':2967',
> qmcharge = -1,
> qm_theory = 'DFTB3',
> qmshake = 0, diag_routine = 0,
> qm_ewald = 1, qm_pme = 1,
> printcharges = 1, printdipole = 1, verbosity = 0 / DISANG=dist.RST
The order of the input blocks is given in Section 21.5 of the Reference Manual. You need to put the &qmmm namelist right after the &cntrl one, followed the by "varying conditions" (&wt sections), followed by the DISANG card.
If you still have trouble, be sure to provide your modified input file.
....dac
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Received on Thu Apr 20 2023 - 01:00:02 PDT
