Hi,
As prof. Simmerling says, a protein in water should behave fine unless
there is something odd in your structure. In former emails the error
involved atoms 919 and 920, now 874 and 875. Given that your protein has
177 residues I think it is very unlikely those numbers refer atoms in
solvent as you said before.
Please provide more details about your work: what force field are you
using? do you have any ligands? does your structure have a PDB code
so we can examine it? It would be interesting to see your input file too.
Regards-
On Wed, Apr 1, 2020 at 10:14 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> What is your starting structure? Did your amber installation pass the
> tests? A protein in water should be fine unless there is an issue with the
> structure. Please try to share all details of what you are simulating, how
> you built it, and anything else that might help people know what you are
> doing and why it may not work properly.
>
> On Wed, Apr 1, 2020, 8:40 AM Sunita Patel <sunita.patel.cbs.ac.in> wrote:
>
> > Hi David,
> >
> > I submitted the job several times and it was giving the same problem.
> Today
> > I submit the job and got the following error.
> > I am simulating a protein having 177 residues with water and ions. So it
> is
> > not a small molecule.
> > Do these numbers imply the atom ids?
> > Can I say that my minimization is not proper?
> >
> > Thank you so much for your help
> > Sunita
> >
> > -----------------------
> > vlimit exceeded for step 936; vmax = 12883.8309
> >
> > Coordinate resetting (SHAKE) cannot be accomplished,
> > deviation is too large
> > NITER, NIT, LL, I and J are : 0 0 421 874 875
> >
> > Note: This is usually a symptom of some deeper
> > problem with the energetics of the system.
> > --------------------------
> >
> >
> > On Mon, Mar 30, 2020 at 12:25 PM David Sáez <davidsaez.udec.cl> wrote:
> >
> > > Hi,
> > >
> > > did you solve the issue? If atom 920 is part of the solvent I guess you
> > are
> > > modelling a small molecule. As Carlos Simmerling asked before, are you
> > > using new parameters in the description of this solute?
> > >
> > > David.
> > >
> > > On Sun, Mar 29, 2020 at 1:11 AM Sunita Patel <sunita.patel.cbs.ac.in>
> > > wrote:
> > >
> > > > Dear Users,
> > > >
> > > > When I am doing NPT equilibration, I am getting the message "
> > Coordinate
> > > > resetting (SHAKE) cannot be accomplished" and after that the
> > calculation
> > > is
> > > > stopped.
> > > >
> > > > I finished position restraint NVT without any problem. My pr_NTP.in
> > file
> > > is
> > > > shown below. The pr_npt.out file's output is given below. I tried
> > > > resubmitting the job several times but getting the same message at
> the
> > > same
> > > > step number 800.
> > > >
> > > > How can I rectify this?
> > > >
> > > > Thanks in advance.
> > > >
> > > > Sincerely,
> > > > Sunita
> > > >
> > > > ----------------------------pr_NPT.in--------
> > > > &cntrl
> > > > imin = 0, irest = 1, ntx = 5,
> > > > ntb = 2, pres0 = 1.0, ntp = 1,
> > > > taup = 2.0,
> > > > cut = 10.0, ntr = 0,
> > > > ntc = 2, ntf = 2, ig = -1,
> > > > tempi = 300.0, temp0 = 300.0,
> > > > ntt = 3, gamma_ln = 1.0,
> > > > nstlim = 100000, dt = 0.002,
> > > > ntpr = 100, ntwx = 100, ntwr = 1000
> > > > /
> > > > &ewald
> > > > order = 4,
> > > > /
> > > > -----------------------------
> > > > NSTEP = 700 TIME(PS) = 21.400 TEMP(K) = 300.17 PRESS
> =
> > > > -218.5
> > > > Etot = -74699.8208 EKtot = 19122.0076 EPtot =
> > > > -93821.8284
> > > > BOND = 544.7494 ANGLE = 1427.3090 DIHED =
> > > > 2223.9704
> > > > 1-4 NB = 661.6464 1-4 EEL = 6471.0812 VDWAALS =
> > > > 11607.7526
> > > > EELEC = -116758.3373 EHBOND = 0.0000 RESTRAINT =
> > > > 0.0000
> > > > EKCMT = 8577.8177 VIRIAL = 10409.9257 VOLUME =
> > > > 388345.7996
> > > > Density =
> > > > 0.8201
> > > > Ewald error estimate: 0.9435E-04
> > > >
> > > >
> > >
> >
> ------------------------------------------------------------------------------
> > > >
> > > >
> > > > NSTEP = 800 TIME(PS) = 21.600 TEMP(K) = 298.98
> PRESS =
> > > > -326.6
> > > > Etot = -74794.7684 EKtot = 19046.3671 EPtot =
> > > > -93841.1355
> > > > BOND = 575.3748 ANGLE = 1400.1912 DIHED =
> > > > 2225.2308
> > > > 1-4 NB = 633.8584 1-4 EEL = 6453.8437 VDWAALS =
> > > > 11479.9745
> > > > EELEC = -116609.6089 EHBOND = 0.0000 RESTRAINT =
> > > > 0.0000
> > > > EKCMT = 8477.3787 VIRIAL = 11210.5540 VOLUME =
> > > > 387619.0198
> > > > Density =
> > > > 0.8216
> > > > Ewald error estimate: 0.7500E-04
> > > >
> > > >
> > >
> >
> ------------------------------------------------------------------------------
> > > >
> > > > vlimit exceeded for step 816; vmax = 28847.4477
> > > >
> > > > Coordinate resetting (SHAKE) cannot be accomplished,
> > > > deviation is too large
> > > > NITER, NIT, LL, I and J are : 0 0 436 919 920
> > > >
> > > > Note: This is usually a symptom of some deeper
> > > > problem with the energetics of the system.
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Received on Wed Apr 01 2020 - 07:00:01 PDT
