Hi,
I am trying to run simulations to relax a docked system consisting a drug-like ligand and single-chain peptide.
I run the mininization process successfully and get a rather normal structure for the following heating process.
But odd thing happend when I started the simulation as output files contained no results.
The bottom of output file is like this:
''
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
| # of SOLUTE degrees of freedom (RNDFP): 109509.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 109509. NUM_NOSHAKE = 0 CORRECTED RNDFP = 109509.
| TOTAL # of degrees of freedom (RNDF) = 109509.
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 1274522
| TOTAL SIZE OF NONBOND LIST = 16849795
''
Which missing the supposed to be printed results about equilibration.
Simulation space is suffience for this run.
My input file is :
''
Initial equibilization with protein fixed
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
ig = -1,
gamma_ln = 1.0,
nstlim = 100000,
dt = 0.002,
ntpr = 1000,
ntwx = 1000,
ntwr = 10000,
ioutfm = 1,
/
Keep protein fixed with restrains
10.0
RES 1 538
END
END
''
I tried this simulation both with Amber11 ad Amber16, they got same ouput files as both missing the result part.
Did I write something wrong in the input file?
Where should I check if such things happen?
Thank you very much
Wangjy
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Received on Mon Apr 02 2018 - 02:00:03 PDT
