I think we're getting closer...
since the wild type worked fine and the mutant does not, I'm assuming that
the experimental structure was the wild type? did you need to model the
structure for the mutant? what is different in your protocol between the
one that worked and the one that did not? that should give you a strong
clue...
On Wed, Apr 1, 2020 at 12:36 PM Sunita Patel <sunita.patel.cbs.ac.in> wrote:
> 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 - 10:30:02 PDT
