why is your initial restraint energy so high? if your inpcrd and refc are
the same, the restraint energy should be 0. it's not clear what you have
done.
furthermore, if you use ntx=5 and ntx=1, I would expect non-zero kinetic
energy at step 0. if my memory is right, it should not even report step 0.
are you sure this is the correct sander script and mdin to go along with
this output?
there are many things that can go wrong in equilibration, this is why it's
important to carefully follow the tutorials and learn the problems solving
skills needed for MD.
On Thu, Apr 2, 2009 at 4:12 AM, thirsty <thirstymail.gmail.com> wrote:
> I want to calculate the mm/pbsa between a ligand and a protein. When I run:
>
> $AMBERHOME/exe/sander -O -i density.in -o density.out -p
> ras-raf_solvated.prmtop -c heat.rst \
> -r density.rst -x density.mdcrd -ref heat.rst
> The error happened:
> ---------------------------------------------------
> 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 = 11197800
> | TOTAL SIZE OF NONBOND LIST = 11197800
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> 0.0
> Etot = -170815.7622 EKtot = 0.0000 EPtot =
> -170815.7622
> BOND = 154.6188 ANGLE = 608.1955 DIHED =
> 2270.4872
> 1-4 NB = 913.2979 1-4 EEL = 11917.0978 VDWAALS =
> 48825.5422
> EELEC = -330729.7487 EHBOND = 0.0000 RESTRAINT =
> 95224.7472
> EAMBER (non-restraint) = -266040.5093
> Ewald error estimate: 0.1646E-03
>
> ------------------------------------------------------------------------------
>
>
> NSTEP = 100 TIME(PS) = 0.200 TEMP(K) = 251.84 PRESS =
> 0.0
> Etot = -136672.3541 EKtot = 31241.4860 EPtot =
> -167913.8401
> BOND = 2037.0652 ANGLE = 5657.9467 DIHED =
> 3621.1226
> 1-4 NB = 1494.2678 1-4 EEL = 11687.0045 VDWAALS =
> 37542.1375
> EELEC = -271841.5123 EHBOND = 0.0000 RESTRAINT =
> 41888.1280
> EAMBER (non-restraint) = -209801.9681
> Ewald error estimate: 0.1549E-03
>
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 168; vmax = 49.4150
> vlimit exceeded for step 171; vmax = 99.2573
> vlimit exceeded for step 173; vmax = 33.3404
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 2150 4380 4440
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
>
>
> Here is my density.in file:
>
> heat ras-raf
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=25000,dt=0.002,
> ntc=2,ntf=2,
> cut=8.0, ntb=2, ntp=1, taup=1.0,
> ntpr=500, ntwx=500,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> ntr=1, restraintmask=':1-242',
> restraint_wt=2.0,
> /
>
>
>
> what about it? how should I do?
>
> Thank you!
>
> GuanXin
> 2009.04.02
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>
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Received on Fri Apr 03 2009 - 01:14:00 PDT
