Hi Ross,
It just stops after the 2nd nstep and the minimization doesn't proceed any
further. I'm attaching my minimization output for your reference.
My input script was:
/sander -O -i min_wat.in -o peg5k_wat_min_vac.out -p peg5k_wat.top -c
peg5k_wat.crd -r peg5k_wat_min_vac.rst -ref peg5k_wat.crd
My .crd and .top files are too large to attach to this email, so I've
uploaded them to my web server here:
http://bioengineering.ucsd.edu/~lpeng/peg/peg5k_wat.crd
http://bioengineering.ucsd.edu/~lpeng/peg/peg5k_wat.top
Thanks for your help,
Lili
2008/12/17 Ross Walker <ross.rosswalker.co.uk>
> Hi Lili,
>
>
>
> What do you mean by 'ends'? Do you get any further output? Any error
> messages of any kind? It would also be helpful to see your input file.
>
>
>
> All the best
>
> Ross
>
>
>
> *From:* owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] *On
> Behalf Of *Lili Peng
> *Sent:* Tuesday, December 16, 2008 11:14 PM
> *To:* amber.scripps.edu
> *Subject:* AMBER: AMBER minimization problems
>
>
>
> Hi AMBER,
>
> I'm having trouble minimizing a 5000 Dalton polyethylene glycol molecule
> solvated in a TIP3PBOX 15 water molecules. The output file I get ends after
> the 2nd nstep of 500 (shown below). This is after I've vacuumed minimized
> my molecule (and then solvated it in water). I've attached my water
> minimization file input file. Do anyone know what the problem could be?
>
> Thanks,
> Lili
>
>
> --------------------------------------------------------------------------------
> 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 = 64267381
> | TOTAL SIZE OF NONBOND LIST = 130524253
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 1 -2.0703E+06 1.2881E+01 4.6850E+01 O 255159
>
> BOND = 16.4676 ANGLE = 8.8005 DIHED =
> 158.2966
> VDWAALS = 255110.9185 EEL = -2325481.7410 HBOND =
> 0.0000
> 1-4 VDW = 105.8433 1-4 EEL = -249.6019 RESTRAINT =
> 0.0000
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 500 -2.6528E+06 9.0587E-01 4.5299E+00 H1 309256
>
> BOND = 182580.9181 ANGLE = 4.6033 DIHED =
> 157.3146
> VDWAALS = 382897.9872 EEL = -3218340.8995 HBOND =
> 0.0000
> 1-4 VDW = 103.2430 1-4 EEL = -249.2364 RESTRAINT =
> 3.5502
> EAMBER = -2652846.0697
>
>
>
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Received on Fri Dec 19 2008 - 01:09:30 PST
