AMBER Archive (2006)

Subject: AMBER: mmpbsa: fail to run heat in tutorial A3

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Sun Oct 22 2006 - 12:31:53 CDT


Dear amber members,

I have few problems on tutorial A3 (MMPBSA). First, i found that after i
finished minimization and then run MD. It stop running at heat.in file as
show below. Seconds, i was wondering about the restrain on molecule, should
i restrain both protein and ligands ? or restraint only protein ?. So, any
suggestions will be appreciate.

APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
 using 5000.0 points per unit in tabled values
 TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.3146E-14 at 2.553520
| CHECK d/dx switch(x): max rel err = 0.8129E-11 at 2.782960
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 5776525
| TOTAL SIZE OF NONBOND LIST = 5776525

 NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
0.0
 Etot = -95052.6404 EKtot = 0.0000 EPtot = -
95052.6404
 BOND = 92.1529 ANGLE = 537.9972 DIHED =
2279.5542
 1-4 NB = 914.1070 1-4 EEL = 7868.4067 VDWAALS =
5561.6015
 EELEC = -112306.4599 EHBOND = 0.0000 RESTRAINT =
0.0000
 Ewald error estimate: 0.4077E-03
 ------------------------------------------------------------------------------

 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================

 NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 44.21 PRESS =
0.0
 Etot = -117676.6526 EKtot = 3025.9558 EPtot = -
120702.6085
 BOND = 118.9249 ANGLE = 531.6265 DIHED =
2209.6471
 1-4 NB = 762.8915 1-4 EEL = 7600.9698 VDWAALS =
20022.3297
 EELEC = -152302.8398 EHBOND = 0.0000 RESTRAINT =
353.8418
 EAMBER (non-restraint) = -121056.4502
 Ewald error estimate: 0.3155E-03
 ------------------------------------------------------------------------------

 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================

 NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 18.20 PRESS =
0.0
 Etot = -122672.7204 EKtot = 1245.8666 EPtot = -
123918.5870
 BOND = 130.2379 ANGLE = 534.4423 DIHED =
2201.0884
 1-4 NB = 771.4958 1-4 EEL = 7590.3554 VDWAALS =
21844.6300
 EELEC = -157333.5349 EHBOND = 0.0000 RESTRAINT =
342.6980
 EAMBER (non-restraint) = -124261.2851
 Ewald error estimate: 0.2994E-03
 ------------------------------------------------------------------------------

 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================

 NSTEP = 1500 TIME(PS) = 3.000 TEMP(K) = 17.67 PRESS =
0.0
 Etot = -123204.7958 EKtot = 1209.7972 EPtot = -
124414.5930
 BOND = 134.3610 ANGLE = 562.4678 DIHED =
2216.4080
 1-4 NB = 769.4341 1-4 EEL = 7590.7701 VDWAALS =
22288.6205
 EELEC = -158314.6647 EHBOND = 0.0000 RESTRAINT =
338.0102
 EAMBER (non-restraint) = -124752.6032
 Ewald error estimate: 0.3326E-03
 ------------------------------------------------------------------------------

 NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================

heat.in

File Assignments:
| MDIN: heat.in
| MDOUT: heat.out
|INPCRD: min.rst
| PARM: enz-lig71_solvated.top
|RESTRT: heat.rst
| REFC: min.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: heat.mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 Here is the input file:

heat ras-raf
 &cntrl
  imin=0,irest=0,ntx=1,
  nstlim=25000,dt=0.002,
  ntc=2,ntf=2,
  cut=8.0, ntb=1,
  ntpr=500, ntwx=500,
  ntt=3, gamma_ln=2.0,
  tempi=0.0, temp0=300.0,
  ntr=1, restraintmask=':1-237',
  restraint_wt=2.0,
  nmropt=1
 /
 &wt TYPE='TEMP0', istep1=0, istep2=25000,
  value1=0.1, value2=300.0, /
 &wt TYPE='END' /

Thanks in advance,

Jitrayut Jitonnom, Ph.D.
Dept. of Chemistry,
Computational Simulation,
and Modeling Laboratory (CSML),
Chiang Mai University, Thailand.
Tel: +66(0)6613-4218
Email: jitrayut.018_at_gmail.com <shafinaz_at_bri.nrc.ca>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu