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
>
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Received on Thu Jul 20 2017 - 12:30:02 PDT
