AMBER Archive (2006)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Oct 23 2006 - 10:39:26 CDT

Dear Jitrayut,
 
I don't know why your calculation stopped after 1500 steps. Are you running
the exact same input files and structure as was in the tutorial? The output
you give below is very very different to the output given in the tutorial.
You also seem to have changed the restraint mask for some reason. I
originally restrained residues 1 to 242 which corresponds to the RAS and RAF
protein. The idea being that only the water can move away from the initial
structure during heating. This is to improve the system's stability during
the heating phase. You should check things carefully. Particularly make sure
that your installation of Amber passes all of the tests. Secondly check if
you can run other simulations on your machine. Are you certain it is not
being killed by some wallclock limit on your cluster or machine? Are there
any errors generated to your queuing system log file or to nohup.out (or any
other logfile you wrote standard error to)?
 
Secondly with regards to restraining the ligand. In section 1 just below the
first image on the page it states:
 
For the purposes of this tutorial and for the sake of simplicity we will
avoid treating the GTP molecule in the calculation since this would require
the setup of new parameters for this compound and is beyond the scope of
this tutorial
 
Thus the GTP "ligand" is not present in the structures used in this
tutorial. Hence the restraints are only on the two proteins. However, if the
ligand was there then yes you would probably want to restrain that as well.
 
All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> | PGP Key
available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

 

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
jitrayut jitonnom
Sent: Sunday, October 22, 2006 10:32
To: amber_at_scripps.edu
Subject: AMBER: mmpbsa: fail to run heat in tutorial A3

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:  <mailto:shafinaz_at_bri.nrc.ca> jitrayut.018_at_gmail.com

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