You should be able to use only restraintmask etc and not need the part
after &end. Turn off constant pressure for minimization (ntp).
Then, get rid of anything except things you are sure you want to change
from defaults. For those, check to make aure the spelling is correct.For
example, dielc, scee and others should not be necessary unless you eant to
do something unusual. You should be able to set only a few flags. Then,
when it works, add back things you really want.
Also check the amber page for working examples in the very first tutorials.
On Mon, Jun 10, 2024, 12:55 PM Collin Nisler via AMBER <amber.ambermd.org>
wrote:
> Hello Amber community, I apologize for the elementary question, but I have
> tried everything by reading the manual, checking mailing lists, and
> modifying the syntax every way I could conceive and still cannot correct
> the error. I am trying to run a minimization of a solvated RNA complex with
> the following input file:
>
> minimization of water/ions holding RNA
> &cntrl
> imin=1, ntx=1, drms=0.01, ntmin=1,
> dielc=1.0, ntrx=1, ntxo=1, nscm=100,
> ntwprt=0, ntb=2, ntp=2,
> irest=0, cut=9.0,
> ntpr=100, ntwx=100, ntwe=100,
> nsnb=10, maxcyc=10000, ncyc=10000,
> ntt=0, ntr=1, scee=1.2, vlimit=20.0,
> restraintmask = ':1-25',
> restraint_wt = 200,
> &end
> Hold RNA fixed
> 200
> RES 1 25
> END
> END
>
> I run using the command
>
> sander -O -i min1-3.in -o min1-3.out -p
> NonEnz-DirectCoord-12-6-4-Final-1264-4.prmtop -c
> NonEnz-DirectCoord-12-6-4-Final-1264-4-2.rst7 -ref
> NonEnz-DirectCoord-12-6-4-Final-1264-4-2.rst7 -r min1.rst7
>
> And get the classic "error in reading namelist cntrl" error.
>
> I've tried running without the constraints on the RNA just to see if the
> issue was coming from there, and have changed the syntax of the input file
> (used / instead of &end, changed the spacing, etc.) and I still get the
> same error. Any assistance would be greatly appreciated.
>
> Collin
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jun 10 2024 - 10:30:01 PDT
