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
> >
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Received on Tue Aug 01 2017 - 08:00:02 PDT
