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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Received on Mon Jul 12 2021 - 00:30:02 PDT
