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.
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 03 2020 - 19:00:03 PDT
