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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Received on Mon Jun 10 2024 - 10:00:01 PDT
