Dear Carlos,
My starting structure is a well folded gS-crystallin with single residue
mutant. gS-crystallin wild type protein didn't give any problem. Its
running fine.
The topology and parameter files are generated using tleap program of
AMBER18. However, I am running simulation in AMEBR14. AMBER14 simulation
passed all the tests. But AMBER18 serial installation passed all serial
tests. I had problem with amber 18 parallel so am using AMBER14.
Thank you so much for your help.
Sunita
On Wed, Apr 1, 2020 at 6:46 PM 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 - 10:00:02 PDT
