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 - 11:30:01 PDT
