AMBER Archive (2009)

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

From: Chris Whittleston (csw34_at_cam.ac.uk)
Date: Mon Jul 27 2009 - 15:04:14 CDT

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
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