since the VDW energy is the problem, you should use a visualization program
to look for atomic overlaps- especially near atom H56, which has a very high
force (GMAX).
On Wed, Mar 17, 2010 at 11:04 AM, Hyma vathi <hymavathi.niper.gmail.com>wrote:
> 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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Received on Wed Mar 17 2010 - 08:30:08 PDT
