AMBER Archive (2009)

Subject: Re: [AMBER] Using idecomp=3 with igb=10 (PB)

From: Chris Whittleston (csw34_at_cam.ac.uk)
Date: Tue Jul 28 2009 - 05:54:09 CDT

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_at_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_at_cam.ac.uk>
> > An: amber_at_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_at_cam.ac.uk
> > Tel: +44 (0)1223 336423
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
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-- 
Chris Whittleston
Department of Chemistry
University of Cambridge
Lensfield Road, Cambridge, CB2 1EW
Email: csw34_at_cam.ac.uk
Tel: +44 (0)1223 336423
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