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
> 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 Thu Jul 20 2017 - 13:30:02 PDT
