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
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|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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http://www.rosswalker.co.uk/> | PGP Key
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
jitrayut jitonnom
Sent: Sunday, October 22, 2006 10:32
To: amber.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.bri.nrc.ca> jitrayut.018.gmail.com
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Received on Wed Oct 25 2006 - 06:07:13 PDT
