try doing this with a single CPU core and not using MPI. it tends to be
better at writing error messages to the mdout file.
On Tue, Aug 1, 2017 at 10:48 AM, Alonso Martinez, Diego <
diego.alonso-martinez12.imperial.ac.uk> wrote:
> Dear Amber users,
>
> Bill, many thanks for your help.
>
> I’ve tried to run 10K dynamics without restraints to relax the things as
> you proposed. To do so, after running the minimization as before, I run a
> heating step from 0 to 10 K followed by a 10K run. However, instead of just
> heating to 10K, the temperature keeps on rising gradually reaching 240.41K
> instead of the requested 10K, at which point it stops.
>
> I forgot to mention that the structure is formed by protein subunits each
> derived from an homology model and put together based on an homologous
> protein complex. I wonder if the issue is that I have bad contacts in the
> initial structure and if so how to fix it.
>
> The script I used to do the heating during 500 ps from 0 to 10K with no
> restraints was:
>
> &cntrl
> imin=0,
> irest=0,
> ntx=1,
> nstlim=250000, dt=0.002, ntc=2,
> ntf=2,
> tol=0.0000001,
> cut=10.0,
> ntb=1,
> ntpr=1,
> ntwx=1,
> ntt=3,
> gamma_ln=1.0,
> ig=-1,
> ntr=0,
> ntp=0,
> ioutfm=1, nmropt=1,
> ntxo=2,
> /
> &wt TYPE='TEMP0', istep1=0, istep2=250000,
> value1=0.0, value2=10.0 /
> &wt TYPE='END' /
>
> The output of the first step was:
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> 0.0
> Etot = -377171.6447 EKtot = 0.0000 EPtot =
> -377171.6447
> BOND = 21999.6885 ANGLE = 5590.9971 DIHED =
> 11036.2669
> 1-4 NB = 4130.5966 1-4 EEL = 25899.7724 VDWAALS =
> 22637.8494
> EELEC = -468466.8157 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.9785E-03
> ------------------------------------------------------------
> ------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
>
>
> Whereas the last step after which the simulation stopped was:
>
> NSTEP = 65 TIME(PS) = 0.130 TEMP(K) = 240.41 PRESS =
> 0.0
> Etot = -389058.7206 EKtot = 68279.1807 EPtot =
> -457337.9013
> BOND = 3093.9788 ANGLE = 6161.3515 DIHED =
> 11719.1974
> 1-4 NB = 3272.8328 1-4 EEL = 24198.5591 VDWAALS =
> 54660.9222
> EELEC = -560444.7431 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.2856E-03
> ------------------------------------------------------------
> ------------------
>
> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
> ============================================================
> ===================
>
> Do you have any input about the reason why you think this is happening?
>
> Any input is welcome. Many thanks for your help.
>
> Diego
>
>
>
>
> On 20/07/2017, 21:00, "Bill Ross" <ross.cgl.ucsf.edu> wrote:
>
> If you do as I advise, you might immediately see what the problem is.
>
> Bill
>
> <div>-------- Original message --------</div><div>From: "Alonso
> Martinez, Diego" <diego.alonso-martinez12.imperial.ac.uk>
> </div><div>Date:07/20/2017 12:33 PM (GMT-08:00) </div><div>To: AMBER
> Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] Sander
> doing the minimisation but stopping at the first
> heating step, not generating rst or nc files </div><div>
> </div>Dear all,
>
> Many thanks for your time and help.
>
> The system had already undergone minimisation before I started this
> heating run. Perhaps I didn’t choose the adequate parameters for
> minimization or it is not sufficient? The two round of minimization that I
> used for this system were:
>
> Round #1:
> Minimise complex with 2 kcal mol restraints in 10000 steps
> &cntrl
> imin=1,maxcyc=10000,ncyc=3000,
> cut=12.0,ntb=1,
> ntc=2,ntf=2,
> ntpr=100,
> ntr=1,
> /
> Allowing only water and the counterions to move with 2 kcal mol
> restraint
> 2.0
> RES 1 857
> END
> END
>
> Round #2:
> Minimise complex with no restraints
> &cntrl
> imin=1,maxcyc=10000,ncyc=3000,
> cut=12.0,ntb=1,
> ntc=2,ntf=2,
> ntpr=100,
> ntr=0,
> /
>
> Please let me know if you have any further inputs. Many thanks.
>
> Best wishes,
> Diego
>
>
>
> On 20/07/2017, 20:23, "Bill Ross" <ross.cgl.ucsf.edu> wrote:
>
> I would try running plain 10K dynamics without restraints to relax
> things. View the trajectory, and you might see where the problem
> is with
> your restrained model.
>
> Bill
>
>
> On 7/20/17 12:19 PM, Alonso Martinez, Diego wrote:
> > Dear all,
> >
> > In addition to what I previously described, the following
> information also appeared:
> >
> > vlimit exceeded for step 40; vmax = 33.6600
> >
> > Coordinate resetting (SHAKE) cannot be accomplished,
> > deviation is too large
> > NITER, NIT, LL, I and J are: 0 0 6457 12945
> 12946
> >
> > Note: This is usually a symptom of some deeper
> > problem with the energetics of the system.
> >
> > Best wishes,
> > Diego
> >
> > On 20/07/2017, 19:58, "Alonso Martinez, Diego" <
> diego.alonso-martinez12.imperial.ac.uk> wrote:
> >
> > Dear all,
> >
> > Many thanks for your inputs.
> >
> > I’ve followed your recommendations. The simulation now runs
> up to 40 steps where it stops. The output for step 0 is:
> >
> > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) =
> 0.00 PRESS = 0.0
> > Etot = -377171.9116 EKtot = 0.0000 EPtot
> = -377171.9116
> > BOND = 22001.3894 ANGLE = 5591.1333 DIHED
> = 11036.2664
> > 1-4 NB = 4130.6427 1-4 EEL = 25899.8412
> VDWAALS = 22638.7966
> > EELEC = -468469.9812 EHBOND = 0.0000
> RESTRAINT = 0.0000
> > Ewald error estimate: 0.9785E-03
> > ------------------------------
> ------------------------------------------------
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000
> Torsion = 0.000
> >
> >
> > And the output for the last step (40) is:
> >
> > NSTEP = 40 TIME(PS) = 0.080 TEMP(K) =
> 158.88 PRESS = 0.0
> > Etot = -382330.0469 EKtot = 45123.8992 EPtot
> = -427453.9461
> > BOND = 8652.6936 ANGLE = 4998.5073 DIHED
> = 11097.1310
> > 1-4 NB = 3798.8621 1-4 EEL = 25049.1304
> VDWAALS = 47662.3745
> > EELEC = -542003.8679 EHBOND = 0.0000
> RESTRAINT = 13291.2230
> > EAMBER (non-restraint) = -440745.1691
> > Ewald error estimate: 0.5425E-03
> > ------------------------------
> ------------------------------------------------
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000
> Torsion = 0.000
> >
> >
> > What surprised me the most about this outcome is the fact
> that I set the temperature to increase from 0 to 100 K but it does increase
> up to 158.88K. Do you have any input about why this could be happening?
> Many thanks.
> >
> > Best wishes,
> > Diego
> >
> >
> > On 20/07/2017, 14:40, "Carlos Simmerling" <
> carlos.simmerling.gmail.com> wrote:
> >
> > also run with single thread, not MPI.
> >
> > On Thu, Jul 20, 2017 at 9:22 AM, Adrian Roitberg <
> roitberg.ufl.edu> wrote:
> >
> > > Try setting ntpr=1 and ntwx=1 and see if you ever go
> beyond the first
> > > step and what happens.
> > >
> > > Right now you have them set to 5000, so lots of
> things could have
> > > happened between those steps.
> > >
> > > adrian
> > >
> > >
> > > On 7/20/17 9:05 AM, Alonso Martinez, Diego wrote:
> > > > Dear Amber users,
> > > >
> > > > I am trying to obtain a MD trajectory of a
> DNA-protein-metal-ligand
> > > complex.
> > > >
> > > > To prepare the inpcrd and prmtop files, I followed
> the following
> > > approach: first, I’ve prepared PDB files of each of
> the elements of the
> > > simulation: the protein and the DNA with the H++
> webserver, the ligand and
> > > metal with antechamber. Then, I joined all the pdb
> files into one with the
> > > cat command, to then generate the inpcrd and prmtop
> files of the complex
> > > with tleap.
> > > >
> > > > The tleap input file was as follows:
> > > >
> > > > source leaprc.protein.ff14SB
> > > > source leaprc.DNA.OL15
> > > > source leaprc.water.tip3p
> > > > source leaprc.gaff2
> > > > CPF = loadmol2 CPF.mol2
> > > > loadamberparams CPF.frcmod
> > > > loadamberparams frcmod.ions234lm_126_tip3p
> > > > mol = loadpdb Gyrase_complex_fixed.pdb
> > > > savepdb mol Gyrase_complex_dry.pdb
> > > > saveamberparm mol Gyrase_complex_dry.prmtop
> Gyrase_complex_dry.inpcrd
> > > > solvateoct mol TIP3PBOX 15.0
> > > > addions mol Na+ 0
> > > > addions mol Cl- 0
> > > > savepdb mol Gyrase_complex_solv.pdb
> > > > saveamberparm mol Gyrase_complex_solv.prmtop
> Gyrase_complex_solv.inpcrd
> > > > quit
> > > >
> > > > The method used to parametrize the metal ion is the
> nonbonded model as
> > > we want to observe if the metal ion exits the binding
> site upon mutations
> > > in the protein. The parametrization was checked with
> parmed.
> > > >
> > > > Inpcrd and prmtop files of the solvated complex
> were then generated.
> > > Then, we proceeded with an energy minimization using
> sander.MPI, followed
> > > by heating with sander.MPI as well. The minimization
> run fine, at least
> > > when compared to previously successful minimizations.
> However, when it
> > > passed to the heating, the mdout file only prints the
> first step and does
> > > not continue the simulation after that, not even
> generating a trajectory
> > > file. The mdout file was:
> > > >
> > > > NSTEP = 0 TIME(PS) = 0.000 TEMP(K)
> = 0.00 PRESS =
> > > 0.0
> > > > Etot = -393779.1731 EKtot =
> 0.0000 EPtot =
> > > -393779.1731
> > > > BOND = 23619.4348 ANGLE =
> 5814.7119 DIHED =
> > > 11047.5656
> > > > 1-4 NB = 4193.6173 1-4 EEL =
> 25963.2849 VDWAALS =
> > > 29449.7359
> > > > EELEC = -493867.5237 EHBOND =
> 0.0000 RESTRAINT =
> > > 0.0000
> > > > Ewald error estimate: 0.7721E-03
> > > > NMR restraints: Bond = 0.000 Angle =
> 0.000 Torsion =
> > > 0.000
> > > > ==============================
> ==============================
> > > ===================
> > > >
> > > > After which no more steps are printed. The program
> just exits and
> > > doesn’t generate trajectory or restart files to
> continue to the next
> > > heating step. The heating input file was:
> > > >
> > > > &cntrl
> > > > imin=0,
> > > > irest=0,
> > > > ntx=1,
> > > > nstlim=250000, dt=0.002,
> > > > ntc=2, ntf=2,
> > > > tol=0.0000001,
> > > > cut=10.0, ntb=1,
> > > > ntpr=5000, ntwx=5000,
> > > > ntt=3, gamma_ln=1.0,
> > > > ig=-1,
> > > > ntr=1,
> > > > ntp=0,
> > > > ioutfm=1,
> > > > nmropt=1,
> > > > ntxo=2,
> > > > /
> > > > &wt TYPE='TEMP0', istep1=0, istep2=250000,
> > > > value1=0.0, value2=100.0 /
> > > > &wt TYPE='END' /
> > > > Hold protein and ligand fixed
> > > > 10.0
> > > > RES 1 857
> > > > END
> > > > END
> > > >
> > > > I’ve tried fixing this issue by removing the energy
> constraints and
> > > changing sander for pmemd but none of these options
> work. Could you please
> > > let me know if you had any issue like this and if so
> propose possible
> > > solutions? Many thanks for your help.
> > > >
> > > > Best wishes,
> > > > Diego
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > --
> > > Dr. Adrian E. Roitberg
> > > University of Florida Research Foundation Professor
> > > Department of Chemistry
> > > University of Florida
> > > roitberg.ufl.edu
> > > 352-392-6972
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Aug 01 2017 - 08:00:03 PDT
