I'm sorry, ntr=1 is for positional restraints and not the nmr restraints
that you are using. you already have nmropt=1 and should not add ntr=1 as I
suggested.
does it work if you remove the &qmmm section and ifqnt? that can help debug
the input.
the disang statement may need to go immediately after the weight change,
but I am not positive in your case.
On Wed, Apr 19, 2023 at 3:32 PM Abdullah Bin Faheem via AMBER <
amber.ambermd.org> wrote:
> 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 - 13:00:03 PDT
