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.gmail.com <shafinaz.bri.nrc.ca>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Oct 25 2006 - 06:07:05 PDT
