vlimit errors in simulations with ligands are often due to problems in the
ligand parameters. It can be very helpful to run a simulation without the
ligand and see if problems still occur.
look at the atoms i and j that are listed in the error message- where are
these in the structure? that can help you narrow down the problem.
also, your restraint energy is always 0. Check your output file and see if
Amber is actually reading your restraints and applying them. The energy
should not be zero.
On Mon, Jul 12, 2021 at 3:06 AM Sadaf Rani <sadafrani6.gmail.com> wrote:
> Dear Amber users
> Could you please help me to solve the below-mentioned problem:-
> I am doing a simulation of protein-ligand complex starting from
> minimization which I carried out in 4 steps by keeping restrain of 25kcal
> on solute and slowly removing in 4th minimization with the following
> protocol
> Min1.in
> First Minimization with Cartesian restraints for the solute
> &cntrl
> imin=1, maxcyc=100000,
> ntmin=1, ncyc= 10000,
> ntpr=5,
> ntr=1,
> &end
> Group input for restrained atoms
> 25.0
> RES 1 492
> END
> END
>
> I got a LINMIN failure error in all minimization steps.
> At 4th run of minimization
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 56920 -4.3621E+05 6.3372E-03 6.5170E-01 C 1435
>
> BOND = 34324.2522 ANGLE = 1224.2190 DIHED =
> 5828.5902
> VDWAALS = 88288.1810 EEL = -584472.7522 HBOND =
> 0.0000
> 1-4 VDW = 1626.2805 1-4 EEL = 16970.9196 RESTRAINT =
> 0.0000
>
> .... RESTARTED DUE TO LINMIN FAILURE ...
>
> Similarly, I did 400ps of Heating (NVT ensemble) following the same
> strategy (keeping solute at 25 kcal restraints and slowly removing at 4th
> step using a time step of 0.0005 and increasing temperature from 0 to 298K
> (in 4 steps), nput file for first step is as below:-
> Heating up the system equilibration stage 1
> &cntrl
> nstlim=200000, dt=0.0005, ntx=1, irest=0, ntpr=500, ntwr=500, ntwx=500,
> tempi =0.0, temp0=100.0, ntt=3, tautp=2.0, ig=-1 gamma_ln=5,
>
> ntb=1, ntp=0,
>
> ntc=2, ntf=2,
> nrespa=2,
> &end
> Group input for restrained atoms
> 25.0
> RES 1 492
> END
> END
>
> I got the following result at 4th step of Heating:-
> A V E R A G E S O V E R 100000 S T E P S
>
>
> NSTEP = 200000 TIME(PS) = 100.000 TEMP(K) = 297.75 PRESS =
> 0.0
> Etot = -260448.3982 EKtot = 63880.5754 EPtot =
> -324328.9735
> BOND = 1528.8513 ANGLE = 4064.1654 DIHED =
> 6512.2812
> 1-4 NB = 1847.4515 1-4 EEL = 16995.5142 VDWAALS =
> 40882.0692
> EELEC = -396159.3063 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> Ewald error estimate: 0.4019E-04
>
> Followed by 400ps of equilibration in NPT ensemble in 4 steps as I did in
> Heating with following input at first step:-
> Constant pressure constant temperature equilibration stage 1
> &cntrl
> imin=0, nstlim=200000, dt=0.0005, ntx=5, irest=1, ntpr=5000, ntwr=5000,
> ntwx=5000,
> temp0=300.0, ntt=3, taup=2.0, gamma_ln=5,
>
> ntb=2, ntp=1, pres0 = 1.0,
>
> ntc=2, ntf=2,
>
> nrespa=1,
> &end
> Group input for restrained atoms
> 25.0
> RES 1 492
> END
> END
> I slowly removed restrained mask in 4 steps, and got the following result
> at 4th step of pressure equilibration:-
>
> A V E R A G E S O V E R 40 S T E P S
>
>
> NSTEP = 200000 TIME(PS) = 500.000 TEMP(K) = 299.84 PRESS =
> 11.0
> Etot = -265475.8456 EKtot = 64329.0144 EPtot =
> -329804.8599
> BOND = 1523.5838 ANGLE = 4076.4231 DIHED =
> 6514.3234
> 1-4 NB = 1858.7886 1-4 EEL = 16955.3963 VDWAALS =
> 41889.9791
> EELEC = -402623.3542 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 29170.9234 VIRIAL = 28918.2684 VOLUME =
> 1061130.1795
> Density =
> 1.0107
> Ewald error estimate: 0.3736E-04
>
> ------------------------------------------------------------------------------
> After this, I started the Production run with below-mentioned input:-
>
> Constant pressure constant temperature production run
> &cntrl
> nstlim= 50000000, imin=0, dt=0.002, ntx=5, irest=1, ntpr=5000, ntwr=5000,
> ntwx=5000,
> temp0=298.0, ntt=3, tautp=2.0, gamma_ln=5.0,
>
> ntb=2, ntp=1,
>
> ntc=2, ntf=2,
>
> nrespa=1,
> &end
>
> However, the production run stops with the following error message:-
>
>
> NSTEP = 170000 TIME(PS) = 840.000 TEMP(K) = 298.51 PRESS =
> -32.3
> Etot = -265005.5264 EKtot = 64044.7731 EPtot =
> -329050.2995
> BOND = 1610.1084 ANGLE = 4231.8577 DIHED =
> 6562.7971
> 1-4 NB = 1855.7003 1-4 EEL = 17043.0730 VDWAALS =
> 41568.4437
> EELEC = -401922.2797 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 29151.3974 VIRIAL = 29891.3819 VOLUME =
> 1060223.4767
> Density =
> 1.0116
> Ewald error estimate: 0.4892E-05
>
> ------------------------------------------------------------------------------
>
> vlimit exceeded for step 172777; vmax = 22.2596
> vlimit exceeded for step 172778; vmax = 493.9713
>
> Coordinate resetting cannot be accomplished,
> deviation is too large
> iter_cnt, my_bond_idx, i and j are : 3 32 8054 8053
>
> Could you please suggest to me how I should solve this problem?
> Regards
> Sadaf
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>
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Received on Mon Jul 12 2021 - 08:00:02 PDT
