AMBER Archive (2006)

Subject: RE: AMBER: GBSA EGB = NaN

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Aug 18 2006 - 17:11:52 CDT

Dear William,

I was more interested in seeing the mdin file greated by mmpbsa. Can you run
the calculation manually outside of the mm-pbsa script. What happens in this
case?

There is nothing that looks strange in your output files so it is unlikely
that you have a bad structure. Do the tests cases all pass? Have you tried
setting up a simple GB calculation of your system independently of mmpbsa
and verified that this give the same problem?

I would also try recreating the prmtop file and then also taking a look at
the section labelled:

%FLAG RADII
%FORMAT(5E16.8)

Does anything look weird here. Most of these numbers should be around 0.1 to
2.0. I would pay close attention to anything that is not.

Also which version of GB are you using? I know there can be some issues with
IGB=1 or 2 although I forget specifically what the issues are - perhaps
someone else on the list can contribute here. If you are using IGB=1 or 2
try using IGB=5 and see if this fixes the problem.

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 | PGP Key available on request |

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of William Wei
> Sent: Friday, August 18, 2006 08:12
> To: amber_at_scripps.edu
> Subject: Re: AMBER: GBSA EGB = NaN
>
> 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_at_rosswalker.co.uk>
> To: <amber_at_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_at_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_at_scripps.edu
> > > [mailto:owner-amber_at_scripps.edu] On Behalf Of William Lianhu Wei
> > > Sent: Thursday, August 17, 2006 19:31
> > > To: amber_at_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_at_utoronto.ca
> > > University of Toronto weilianhu_at_hotmail.com
> > > 19 Russell St.
> > > Toronto, Ontario
> > > M5S 2S2,Canada
> > > --------------------------------------------------------------
> > > ---------
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> > > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> > >
> >
> >
> >
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>
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