Dear Amber users,
I am trying to minimise a protein which has cofactor NAP and ligand. I was
able to generate the prmtop and inpcrd files but upon minimisation, the
process is getting aborted and it is giving the following output. Can
anyone please give where the error is, I am attaching the files along with
this mail. Thank you in advance.
This is the min.in file
minimise protein
&cntrl
imin=1,
maxcyc=1000,
ncyc=500,
ntb=1,
ntr=1,
cut=10.0
/
Hold protein fixed
500
RES 1 317
END
END
Out file
4. RESULTS
--------------------------------------------------------------------------------
---------------------------------------------------
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 = 10571808
| TOTAL SIZE OF NONBOND LIST = 10571808
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 1.4117E+11 H56 5054
BOND = 279.7583 ANGLE = 1287.0123 DIHED =
3080.5897
VDWAALS = NaN EEL = NaN HBOND =
0.0000
1-4 VDW = 1576.5396 1-4 EEL = 14107.7055 RESTRAINT =
0.0000
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- application/octet-stream attachment: NAP.mol2
- application/octet-stream attachment: ZST.mol2
Received on Wed Mar 17 2010 - 08:30:04 PDT
