Hi Carlos,
Thanks.
Is this mutation a standard amino acid?
>
The simulation is on all standard amino acids.
>
> If the wild type runs and the mutant does not, it is most likely having to
> do with the mutation, either the parameters or structure. I encourage you
> to compare each step of your protocol in detail. Also examine the initial
structure from pymol, and the last md restart.
I will do this check.
> Focus first on the atoms
> that were listed as the problem before.
ok
> If you are not getting good error
> outputs, switch to the cpu code, and then switch to non-parallel cpu code.
>
This I didn't understand.
Thanks again.
Sunita
>
> On Sat, Apr 4, 2020, 2:16 PM Sunita Patel <sunita.patel.cbs.ac.in> wrote:
>
> > Hi All,
> >
> > Thanks. That was a typo mistake. The problem still exists.
> > I did the whole thing again starting from building the structure. Pymol
> was
> > used to generate the single mutation in the protein. After that I
> minimized
> > the structure and subsequently added water and ions and further minimized
> > the whole system. Further I did position restraint molecular dynamics
> under
> > NVT condition. All the steps succeeded without any problem. But when I
> ran
> > molecular dynamics under NPT condition after 5300 steps it was not
> > proceeding. The status shows that simulation is running. But actually
> that
> > is not running. The output file did not generate any error message this
> > time. But instead generated a "core.224886" binary file which I can not
> see
> > what is inside.
> >
> > I am not able to know now where the problem is. I need your help please.
> >
> > Sincerely,
> > Sunita
> >
> >
> >
> >
> > On Sat, Apr 4, 2020 at 7:28 AM David Sáez <davidsaez.udec.cl> wrote:
> >
> > > The line at the bottom of your message is correct?
> > >
> > > sander -O -i min_struct.in -p GSC_WT_leap1.prmtop -c
> GSC_WT_leap1.prmtop
> > > -r struct_EM.rst -o struct_EM.out
> > >
> > > Why are you using the prmtop file in the flag -c ? That flag needs a
> > > coordinate file.
> > >
> > > On Fri, Apr 3, 2020 at 10:23 PM Sunita Patel <sunita.patel.cbs.ac.in>
> > > wrote:
> > >
> > > > Dear All,
> > > >
> > > > Thanks Carlos for your help.
> > > > I am not able to solve the problem yet. Now some other problems I am
> > > > getting. The wild type crystallin simulation is running using AMBER14
> > > > sander.MPI without any problem. It finished already 130 ns.
> > > >
> > > > But when am doing energy minimization or position restrain
> > equilibration
> > > > under NVT condition then am getting weird problem. For exactly the
> same
> > > > files I am testing which ran a day before now giving following
> problem.
> > > >
> > > > I did position restraint which worked earlier is nolonger running
> now.
> > > Pls
> > > > have a look on the output. The equilibration is stopped at that
> moment.
> > > > However, final production MD on wild type is still running without
> any
> > > > problem.
> > > >
> > > > Do I need to reinstall AMBER14 ? I need AMBER 18 but last time it
> gave
> > > > parallel installation problem.
> > > > Pls guide I am struct.
> > > >
> > > > Thanks in advance,
> > > > Sunita
> > > >
> > > > ================================test for Energy minimization======
> > > > sander -O -i min_struct.in -p GSC_WT_leap1.prmtop -c
> > > GSC_WT_leap1.prmtop
> > > > -r struct_EM.rst -o struct_EM.out
> > > > At line 820 of file ew_box.F90
> > > > Fortran runtime error: Bad value during integer read
> > > > [sunitap.ycn2 test_gSWT]$ which sander
> > > > ~/softwares/amber14/bin/sander
> > > > ================================
> > > > -----------------------------------test for pr_NVT
> > > > equilibration---------------
> > > >
> > > >
> > > >
> > >
> >
> --------------------------------------------------------------------------------
> > > > 1. RESOURCE USE:
> > > >
> > > >
> > >
> >
> --------------------------------------------------------------------------------
> > > >
> > > > | Flags: MPI
> > > > getting box info from netcdf restart file
> > > > ----------------------------------------
> > > >
> > > >
> > > > On Wed, Apr 1, 2020 at 10:34 PM Carlos Simmerling <
> > > > carlos.simmerling.gmail.com> wrote:
> > > >
> > > > > 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 Sat Apr 04 2020 - 20:00:02 PDT
