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From: Sadaf Rani <sadafrani6.gmail.com>

Date: Mon, 12 Jul 2021 12:06:18 +0500

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

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

Date: Mon, 12 Jul 2021 12:06:18 +0500

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

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

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