Dear Ross,
At the beginning of my calculation, it was running sander with the
snapshots. I did not see anything unusual. My system is not big, as about
6430atoms in my complex. I am using SGI Onyx 3800 with IRIX 6.5 system.
Here is my input file and the output of my complex.
Thank you very much,
William
GBSA input:
.GENERAL
#
PREFIX ODC_OMP
PATH ../sn_test_20/
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
#
COMPT ../ODCase_Com.top
RECPT ../ODCase_Rec.top
LIGPT ../ODCase_Lig.top
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 0
MS 1
#
NM 0
#
############################################################################
####
.DELPHI
#
#
FOCUS 0
INDI 1.0
EXDI 80.0
PERFIL 80.0
SCALE 2
LINIT 1000
BNDCON 4
#CHARGE ../my_amber94_delphi.crg
#SIZE ../my_parse_delphi.siz
CHARGE ../amber94_delphi_OMP.crg
SIZE ../parseres_OMP.siz
#
SURFTEN 0.00542
SURFOFF 0.92
#
############################################################################
####
.GB
#
# GB parameters
#
IGB 4
SALTCON 0.00
EXTDIEL 80.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
############################################################################
####
.MS
#
# Molsurf parameters
#
# PROBE - Radius of the probe sphere used to calculate the SAS.
# RADII - Name of the radii file.
#
PROBE 1.4
#RADII ../atmtypenumbers
RADII ../atmtypenumbers_OMP
#
############################################################################
#####
.PROGRAMS
#
# Program executables and paths
#
#DELPHI /home/gohlke/src/delphi.98/exe.R10000/delphi
DELPHI /aspirin/william/Software/delphi/IRIX/delphi
#
############################################################################
####
Output of my complex:
MM
GB
MS
1
BOND = 1198.5268 ANGLE = 3183.2750 DIHED =
3858.7614
VDWAALS = -3497.1212 EEL = -31925.1169 EGB =
NaN
1-4 VDW = 1484.4497 1-4 EEL = 21392.8129 RESTRAINT =
0.0000
surface area = 15877.709
2
BOND = 1249.4284 ANGLE = 3112.2372 DIHED =
3852.2178
VDWAALS = -3529.7154 EEL = -31904.5266 EGB =
NaN
1-4 VDW = 1476.8527 1-4 EEL = 21318.8379 RESTRAINT =
0.0000
surface area = 15876.309
3
BOND = 1206.7192 ANGLE = 3145.3704 DIHED =
3880.0414
VDWAALS = -3512.8353 EEL = -31834.1365 EGB =
NaN
1-4 VDW = 1508.3817 1-4 EEL = 21321.6349 RESTRAINT =
0.0000
surface area = 15878.668
4
BOND = 1236.1746 ANGLE = 3158.5354 DIHED =
3869.2900
VDWAALS = -3485.6651 EEL = -31855.4143 EGB =
NaN
1-4 VDW = 1461.7513 1-4 EEL = 21376.0072 RESTRAINT =
0.0000
surface area = 15798.397
5
BOND = 1247.7303 ANGLE = 3273.7533 DIHED =
3876.9796
VDWAALS = -3534.9529 EEL = -31871.1197 EGB =
NaN
1-4 VDW = 1458.7460 1-4 EEL = 21307.7514 RESTRAINT =
0.0000
surface area = 15895.754
6
BOND = 1241.4778 ANGLE = 3222.0305 DIHED =
3925.6273
VDWAALS = -3488.7917 EEL = -31868.4341 EGB =
NaN
1-4 VDW = 1480.5582 1-4 EEL = 21310.2085 RESTRAINT =
0.0000
surface area = 15913.447
7
BOND = 1246.3852 ANGLE = 3210.2564 DIHED =
3940.9817
VDWAALS = -3559.4844 EEL = -31873.9004 EGB =
NaN
1-4 VDW = 1471.1604 1-4 EEL = 21342.0148 RESTRAINT =
0.0000
surface area = 15736.376
8
BOND = 1239.2338 ANGLE = 3248.2204 DIHED =
3892.2518
VDWAALS = -3497.6510 EEL = -31832.1607 EGB =
NaN
1-4 VDW = 1449.2936 1-4 EEL = 21270.9055 RESTRAINT =
0.0000
surface area = 15745.638
----- Original Message -----
From: "Ross Walker" <ross.rosswalker.co.uk>
To: <amber.scripps.edu>
Sent: Thursday, August 17, 2006 10:57 PM
Subject: RE: AMBER: GBSA EGB = NaN
> Dear William,
>
> Can you post the input files you used both for equilibration and the GB
part
> of the run. Also include the first few steps of the output file so we can
> look more carefully. What happens if you run the calculation from the
> beginning with GB turned on? E.g. during the initial minimisation - do you
> get a problem here? Also do all the GB test cases work? And how big is
your
> molecule? What is you hardware (compilers, math library etc). I have come
> across bugs in IBM's MASSV library on Blue Gene systems where you would
get
> NaN for GB simulations on more than about 20,000 atoms (vexp on vector
> lengths of > 10^8 gives NaN's) but this is a very specific case. There
could
> be other systems that have bugs in their vector math libraries though. But
> first of all before we jump to conclusions it would be good to see all
your
> input and output files.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.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.
>
> > -----Original Message-----
> > From: owner-amber.scripps.edu
> > [mailto:owner-amber.scripps.edu] On Behalf Of William Lianhu Wei
> > Sent: Thursday, August 17, 2006 19:31
> > To: amber.scripps.edu
> > Subject: AMBER: GBSA EGB = NaN
> >
> > Dear all,
> >
> > I finished molecular dynamics simulation of my system about
> > 3ns. From the
> > energy profile, the system reached equilibrium at about 1.5
> > ns. I was trying
> > to calculate the binding free energy. The trajectories I
> > used was after
> > 1.5ns. No matter which trajectory I used, I always got
> > EGB=NaN (on Complex
> > and receptor), and the program stopped at statistical
> > calculation. The VDW
> > contribution is okay. Does anyone meet this before, or give
> > me any clue for
> > that. In 2004 archive, there is somebody asked this, but
> > there was no reply
> > for this. Thanks in advance.
> >
> > William
> >
> > --
> > --------------------------------------------------------------
> > William Wei Tel: +1-416-946-7551
> > Faculty of Pharmacy Email: william.wei.utoronto.ca
> > University of Toronto weilianhu.hotmail.com
> > 19 Russell St.
> > Toronto, Ontario
> > M5S 2S2,Canada
> > --------------------------------------------------------------
> > ---------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
>
>
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Received on Sun Aug 20 2006 - 06:07:19 PDT
