AMBER Archive (2009)

Subject: Re: [AMBER] Help: An error happened when I calculate mm/pbsa

From: thirsty (thirstymail_at_gmail.com)
Date: Fri Apr 03 2009 - 02:11:19 CDT

I found the mol2 file of the receptor is not integrated, some residues were
disappeared. Did this situation affect the result?

I have rewrite the density.in file.

Thank you
GuanXin
2009/4/3

2009/4/2 Carlos Simmerling <carlos.simmerling_at_gmail.com>

> 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_at_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
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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