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 Fri Apr 03 2020 - 18:30:02 PDT
