Hello Chris,
See this output, you will realize what is the problem out there.
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = ************ EKtot = 0.0000 EPtot = ************
BOND = 27342.0949 ANGLE = 978.1773 DIHED = 1354.4338
1-4 NB = 5277.1875 1-4 EEL = 7145.0848 VDWAALS = ************
EELEC = -9360.5582 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
vlimit exceeded for step 0; vmax = 24186095.7
NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0
Etot = ************ EKtot = 0.0000 EPtot = ************
BOND = 27342.0949 ANGLE = 978.1773 DIHED = 1354.4338
1-4 NB = 5277.1875 1-4 EEL = 7145.0848 VDWAALS = ************
EELEC = -9360.5582 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
A V E R A G E S O V E R 1 S T E P S
NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0
Etot = ************ EKtot = 0.0000 EPtot = ************
BOND = 27342.0949 ANGLE = 978.1773 DIHED = 1354.4338
1-4 NB = 5277.1875 1-4 EEL = 7145.0848 VDWAALS = ************
EELEC = -9360.5582 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0
Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0000
BOND = 0.0002 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
EELEC = 0.0001 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
Total Energy is coming very high. So this system is totally unstable.
You do one thing. This i checked to check the confirmation.
You do one thing.Try minimizing the energy of the system. And then
work your script out. Make the system with stable with lowest feasible
energy.
Ashish
On Tue, Jul 28, 2009 at 6:17 PM, Hannes Kopitz<Hannes.Kopitz.gmx.de> wrote:
> Hi Chris,
>
> Sorry, my mistake. It should be something like ...
>
> ...
> RRES 1 318
> END
> LRES 319 319
> END
> RES 1 319
> END
> END
>
> The RRES and LRES cards define the residues to be considered for decomposition, whereas the RES card defines the residues for the output.
> Moreover you should chose idecomp=1 for a per-residue decomposition. With idecomp=3 you would get a pairwise per-residue decomposition.
> Also set ntmin to 2 and maxcyc to 0, cause you don't really want to perform any minimization step.
> But anyway, for doing a PB decomposition you need AMBR10.
> I hope that helps.
>
> Cheers!
> Hannes
>
> -------- Original-Nachricht --------
>> Datum: Tue, 28 Jul 2009 11:54:09 +0100
>> Von: Chris Whittleston <csw34.cam.ac.uk>
>> An: AMBER Mailing List <amber.ambermd.org>
>> Betreff: Re: [AMBER] Using idecomp=3 with igb=10 (PB)
>
>> Dear Hannes,
>>
>> Thanks for the quick reply! I've tried changing to LRES and RRES and it
>> seems to just suppress the output:
>>
>> FINAL RESULTS
>>
>>
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 1 -1.1108E+04 1.3245E+00 1.4038E+01 HG 2021
>>
>> BOND = 191.2619 ANGLE = 696.4471 DIHED =
>> 2808.3488
>> VDWAALS = -2871.4868 EEL = -23739.7079 EPB =
>> -3329.3383
>> 1-4 VDW = 980.7815 1-4 EEL = 14155.9277 RESTRAINT =
>> 0.0000
>> ECAVITY = 0.0000 EDISPER = 0.0000
>>
>>
>> CHECK DECOMP - TOTAL ENERGIES (w/ REST)
>>
>> INTERNAL= 0.0000
>> VDWAALS = 0.0000 EEL = 0.0000
>> EGB = 0.0000 ESURF = 0.0000
>>
>>
>> CHECK DECOMP - SELF ENERGIES (w/o REST)
>>
>> INTERNAL= 0.0000
>> VDWAALS = 0.0000 EEL = 0.0000
>> EGB = 0.0000 ESURF = 0.0000
>>
>>
>> CHECK DECOMP - INDIRECT ENERGIES (w/o REST)
>>
>> INTERNAL= 0.0000
>> VDWAALS = 0.0000 EEL = 0.0000
>> EGB = 0.0000 ESURF = 0.0000
>>
>>
>> CHECK DECOMP - DIRECT ENERGIES (w/o REST)
>>
>> INTERNAL= 0.0000
>> VDWAALS = 0.0000 EEL = 0.0000
>> EGB = 0.0000 ESURF = 0.0000
>>
>>
>> CHECK DECOMP - REST ENERGIES
>>
>> INTERNAL= 0.0000
>> VDWAALS = 0.0000 EEL = 0.0000
>> EGB = 0.0000 ESURF = 0.0000
>>
>>
>>
>>
>> PRINT PAIR DECOMP - TOTAL ENERGIES
>>
>> resid1 ->resid2 |internal |vdw |eel |pol |sas
>> ======================================================================
>>
>>
>> PRINT PAIR DECOMP - SIDECHAIN ENERGIES
>>
>> resid1 ->resid2 |internal |vdw |eel |pol |sas
>> ======================================================================
>>
>>
>> PRINT PAIR DECOMP - BACKBONE ENERGIES
>>
>> resid1 ->resid2 |internal |vdw |eel |pol |sas
>> ======================================================================
>>
>> It seems that the values for the internal, electrostatic and vdw energies
>> are actually non-zero in the total output, just for the decomposition so I
>> guess it could be that because the PB breakdown is not implemented in
>> AMBER9
>> - I'm just getting zeroes. Thanks for the help, I might try switching to
>> AMBER10 at some point soon :)
>>
>> Best,
>>
>> Chris
>>
>> 2009/7/28 Hannes Kopitz <Hannes.Kopitz.gmx.de>
>>
>> > Dear Chris,
>> >
>> > A decomposition of the PB reaction field energy is implemented from
>> AMBER10
>> > but unfortunately not in AMBER9.
>> >
>> > Nevertheless the values for internal, vdw and eel shouldn't be zero.
>> > Just a guess, you should try it with RRES and LRES instead of RES.
>> >
>> > Cheers!
>> > Hannes
>> >
>> > -------- Original-Nachricht --------
>> > > Datum: Mon, 27 Jul 2009 21:04:14 +0100
>> > > Von: Chris Whittleston <csw34.cam.ac.uk>
>> > > An: amber.ambermd.org
>> > > Betreff: [AMBER] Using idecomp=3 with igb=10 (PB)
>> >
>> > > Dear AMBER users,
>> > >
>> > > I'm currently looking at decomposed per-residue interaction energies
>> in a
>> > > protein-ligand system with a GB solvent model (e.g. igb=1/5) but would
>> > > like
>> > > to be able to use Poisson Boltzmann (igb=10) to compare with some
>> results
>> > > from an MMPBSA calculation of the same system. Unfortunately, I am
>> just
>> > > getting a huge table of 0.000 for every interaction energy.
>> > >
>> > > Here is my SANDER input:
>> > >
>> > > Interaction energy per residue input for SANDER
>> > > &cntrl
>> > > imin = 1,
>> > > idecomp = 3,
>> > > ncyc = 1,
>> > > maxcyc = 1,
>> > > igb = 10,
>> > > ntb = 0,
>> > > cut = 0, <- have also tried 999.9
>> > > /
>> > > &pb
>> > > npopt = 0,
>> > > radiopt = 0
>> > > /
>> > > First set
>> > > RES -1 318
>> > > END
>> > > Second set
>> > > RES 319
>> > > END
>> > > END
>> > >
>> > > I am using modified GLYCAM parameters for a sugar ligand, hence have
>> set
>> > > npopt=0 and radiopt=0. SANDER seems to run ok (it doesn't produce any
>> > > warnings or crash out), but after taking 20 seconds or so calculating
>> > > things
>> > > - it produces a table as follows:
>> > >
>> > >
>> > > PRINT PAIR DECOMP - TOTAL ENERGIES
>> > >
>> > > resid1 ->resid2 |internal |vdw |eel |pol |sas
>> > > ======================================================================
>> > > TDC 1-> 1 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 2 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 3 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 4 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 5 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 6 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 7 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 8 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 9 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 10 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 11 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 12 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 13 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 14 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 15 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 16 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 17 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 18 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 19 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 20 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 21 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 22 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 23 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 24 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 25 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 26 0.000 0.000 0.000 0.000 0.000
>> > > TDC 1-> 27 0.000 0.000 0.000 0.000 0.000
>> > > ...
>> > > ...
>> > > etc (they're all zero)
>> > >
>> > > The total energy however is not zero as can be seen in the output
>> above
>> > > the
>> > > interaction energy table:
>> > >
>> > > NSTEP ENERGY RMS GMAX NAME
>> NUMBER
>> > > 1 -1.1108E+04 1.3245E+00 1.4038E+01 HG
>> 2021
>> > >
>> > > BOND = 191.2619 ANGLE = 696.4471 DIHED =
>> > > 2808.3488
>> > > VDWAALS = -2871.4868 EEL = -23739.7079 EPB =
>> > > -3329.3383
>> > > 1-4 VDW = 980.7815 1-4 EEL = 14155.9277 RESTRAINT =
>> > > 0.0000
>> > > ECAVITY = 0.0000 EDISPER = 0.0000
>> > >
>> > >
>> > > Maximum number of minimization cycles reached.
>> > >
>> > >
>> > > FINAL RESULTS
>> > >
>> > >
>> > >
>> > > NSTEP ENERGY RMS GMAX NAME
>> NUMBER
>> > > 1 -1.1108E+04 1.3245E+00 1.4038E+01 HG
>> 2021
>> > >
>> > > BOND = 191.2619 ANGLE = 696.4471 DIHED =
>> > > 2808.3488
>> > > VDWAALS = -2871.4868 EEL = -23739.7079 EPB =
>> > > -3329.3383
>> > > 1-4 VDW = 980.7815 1-4 EEL = 14155.9277 RESTRAINT =
>> > > 0.0000
>> > > ECAVITY = 0.0000 EDISPER = 0.0000
>> > >
>> > >
>> > > CHECK DECOMP - TOTAL ENERGIES (w/ REST)
>> > >
>> > > INTERNAL= 0.0000
>> > > VDWAALS = 0.0000 EEL = 0.0000
>> > > EGB = 0.0000 ESURF = 0.0000
>> > >
>> > >
>> > > CHECK DECOMP - SELF ENERGIES (w/o REST)
>> > >
>> > > INTERNAL= 0.0000
>> > > VDWAALS = 0.0000 EEL = 0.0000
>> > > EGB = 0.0000 ESURF = 0.0000
>> > >
>> > >
>> > > CHECK DECOMP - INDIRECT ENERGIES (w/o REST)
>> > >
>> > > INTERNAL= 0.0000
>> > > VDWAALS = 0.0000 EEL = 0.0000
>> > > EGB = 0.0000 ESURF = 0.0000
>> > >
>> > >
>> > > CHECK DECOMP - DIRECT ENERGIES (w/o REST)
>> > >
>> > > INTERNAL= 0.0000
>> > > VDWAALS = 0.0000 EEL = 0.0000
>> > > EGB = 0.0000 ESURF = 0.0000
>> > >
>> > >
>> > > CHECK DECOMP - REST ENERGIES
>> > >
>> > > INTERNAL= 0.0000
>> > > VDWAALS = 0.0000 EEL = 0.0000
>> > > EGB = 0.0000 ESURF = 0.0000
>> > >
>> > >
>> > > So - I was wondering if anyone could help me understand why I'm just
>> > > getting
>> > > zeroes! My one idea so far is that it is not possible to break down
>> the
>> > PB
>> > > surface energy on a per-atom or per-residue basis and so SANDER is
>> > > printing
>> > > zeros. I'm using AMBER9 with all current bug fixes.
>> > >
>> > > Any and all help is greatly appriciated!
>> > >
>> > > Chris
>> > >
>> > > --
>> > > Chris Whittleston
>> > > Department of Chemistry
>> > > University of Cambridge
>> > > Lensfield Road, Cambridge, CB2 1EW
>> > > Email: csw34.cam.ac.uk
>> > > Tel: +44 (0)1223 336423
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> > --
>> > Neu: GMX Doppel-FLAT mit Internet-Flatrate + Telefon-Flatrate
>> > für nur 19,99 Euro/mtl.!* http://portal.gmx.net/de/go/dsl02
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Chris Whittleston
>> Department of Chemistry
>> University of Cambridge
>> Lensfield Road, Cambridge, CB2 1EW
>> Email: csw34.cam.ac.uk
>> Tel: +44 (0)1223 336423
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Jetzt kostenlos herunterladen: Internet Explorer 8 und Mozilla Firefox 3 -
> sicherer, schneller und einfacher! http://portal.gmx.net/de/go/chbrowser
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Ashish Runthala,
Faculty Division III,
Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 28 2009 - 10:10:03 PDT
