Try to restrain only heavy atoms
On Thu, Jul 20, 2017 at 3:33 PM Alonso Martinez, Diego <
diego.alonso-martinez12.imperial.ac.uk> wrote:
> 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
> > >
> > >
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Received on Thu Jul 20 2017 - 13:00:03 PDT
