On Tue, Jun 24, 2025, MANVENDRA SINGH via AMBER wrote:
>Dear AMBER users, I am using a flat-well restraint in the minimization.
>These are the parameters I used,
># DNA: initial minimization solvent + ions
> &cntrl
> imin = 1,
> maxcyc = 2500,
> ncyc = 1000,
> ntb = 1,
> ntp = 0,
> ntr = 1,
> cut = 10.0,
> ntpr = 500,
> ntwx = 500,
> nmropt = 1,
> /
>Hold the DNA fixed
>500.0
>RES 1 32
>END
>END
>
>&rstlist
> INFILE = 'restraint.in'
>&end
I don't know where the "&rstlist" namelist comes from. Section 22.5 shows
what order the input information needs to be in the mdin file. Section
22.10 describes the file redirection commands.
Immediately after the end of the $crtrl namelist, put your file redirection
commands, probably like
DISANG=restrain.in
Then have the coordinate restraint section. It would, however, be much
simpler to leave this section out entirely, and add "restraint_wt=10,
restraintmask=':1-32'". I suggest a much smaller restraint weight than you
have used.
...hope this helps...dac
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Received on Tue Jun 24 2025 - 11:00:02 PDT
