AMBER Archive (2009)

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

From: Hannes Kopitz (Hannes.Kopitz_at_gmx.de)
Date: Tue Jul 28 2009 - 05:09:01 CDT

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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