Thank you for the suggestion. I tried it out and I get:
5. REFERENCE ATOM COORDINATES
defa
----- READING GROUP 1; TITLE:
DISANG=dist.RST
rfree: End of file on unit 5
Unfortunately sander crashes after this.
Abdullah
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: Thursday, April 20, 2023 4:13 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
try adding ntr=1 to the input.
On Wed, Apr 19, 2023 at 3:10 PM Abdullah Bin Faheem via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>> wrote:
Hello everyone,
I plan to run QM/MM simulations with the DFTB3 semi-empirical method where I wanted to add some NMR restraints to the bonds in the QM region. Nevertheless, when I try to do that I get this in the output file:
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
DUMPFREQ 100 0 0.000000 0.000000 0 0
** No weight changes given **
RESTRAINTS:
No valid redirection requests found
** No restraint defined **
Done reading weight changes/NMR restraints
This implies that the restraints were not read. I further tested this by using very high restraint values, but the atoms that were supposed to be constrained move far apart fairly quickly.
I am currently using AMBER22 (also tested with AMBER18 but it gave same results) and the following are my input files:
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
dist.RST file:
&rst
iat=9340,9341, r1=0.0, r2=0.0, r3=3.5, r4=999, rk2=900.0, rk3=900.0,
/
&rst
iat=9340,9342, r1=0.0, r2=0.0, r3=3.5, r4=999, rk2=900.0, rk3=900.0,
/
I believe there might be something incorrect in my input files but I cant seem to locate the issue. Any suggestions would be of great help.
Thank you for your time.
Abdullah
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Received on Wed Apr 19 2023 - 13:00:02 PDT
