Sun Oct 9 14:16:02 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 14:16:02 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2522 !!! WARNING: HIQ 41 has a net charge of 0.5140 !!! WARNING: SEP 187 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6453719 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -1.621000 45.95900 ymin,ymax (A): 10.27000 56.03500 zmin,zma (A): 10.50600 65.66800 x,y,z range (A): 47.58000 45.76500 55.16200 scale (grids/A): 0.6453719 object centre (A): 22.16900 33.15250 38.08700 number of atom coordinates read : 2522 total number of charged atoms : 2383 net assigned charge : 9.039017 assigned positive charge : 383.4510 centred at (gu) : 88.36527 91.57679 89.96477 assigned negative charge : -374.4128 centred at (gu) : 88.26137 91.45230 89.84451 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7085 nv = 96 ne = 84 npr = 50869 no. pairs analyzed = 50869 no. exposed pairs = 3209 no. arc points = 22218 no. surface atoms = 1073 nbur = 1449 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 381 mr = 3790 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2258 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8398 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2694532E-10 3.0381031E-08 midg,1,midg; midg,igrid,midg -5.6533495E-10 4.3560114E-08 1,midg,midg; igrid,midg,midg 1.9305548E-09 2.0309022E-08 gauss-seidel spectral radius is 0.9875538 estimated iterations to convergence 73 setup time was (sec) 0.5400000 now iterating at: 14:16:02 rms-change max change #iterations 0.1479929 25.09582 at 10iterations 1.4917599E-02 2.057549 at 20iterations 1.4917590E-03 0.2371941 at 30iterations 1.5271713E-04 2.3317337E-02 at 40iterations 1.5706641E-05 2.0847321E-03 at 50iterations finished qdiffx linear iterations at : 14:16:05 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.5706641E-05 2.0847321E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 14:16:06 3.457u 0.164s 0:03.91 92.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 14:16:06 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2522 !!! WARNING: HIQ 41 has a net charge of 0.5140 !!! WARNING: SEP 187 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.936116 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -1.621000 45.95900 ymin,ymax (A): 10.27000 56.03500 zmin,zma (A): 10.50600 65.66800 x,y,z range (A): 47.58000 45.76500 55.16200 scale (grids/A): 1.936116 object centre (A): 22.16900 33.15250 38.08700 number of atom coordinates read : 2522 total number of charged atoms : 2383 net assigned charge : 9.039017 assigned positive charge : 383.4510 centred at (gu) : 85.09503 94.72976 89.89386 assigned negative charge : -374.4128 centred at (gu) : 84.78394 94.35687 89.53342 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 76295 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22218 grid for indexing accessible points = 1.400000 m= 27415 mr = 52584 m= 4121 mr = 19472 m= 228 mr = 2323 m= 5 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 334 time to turn everything in is 0.6200000 number of dielectric boundary points 33627 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 18753 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6453719 object centre at (A) : 22.16900 33.15250 38.08700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8231574E-02 3.4783442E-02 midg,1,midg; midg,igrid,midg -1.5153083E-02 1.5444018E-02 1,midg,midg; igrid,midg,midg 1.9354327E-02 3.7673742E-02 gauss-seidel spectral radius is 0.9986742 estimated iterations to convergence 218 setup time was (sec) 0.9200000 now iterating at: 14:16:07 rms-change max change #iterations 4.325734 173.0732 at 10iterations 2.045570 70.33507 at 20iterations 0.9668674 32.67787 at 30iterations 0.4564067 14.51954 at 40iterations 0.2165139 6.477551 at 50iterations 0.1023425 3.322795 at 60iterations 4.8620328E-02 1.352063 at 70iterations 2.2949891E-02 0.7582798 at 80iterations 1.0895361E-02 0.3243141 at 90iterations 5.1447707E-03 0.1556766 at 100iterations 2.4368395E-03 7.5141907E-02 at 110iterations 1.1560800E-03 3.3691406E-02 at 120iterations finished qdiffx linear iterations at : 14:16:13 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 1.1560800E-03 3.3691406E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 14:16:14 7.652u 0.161s 0:08.10 96.4% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 14:16:14 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2522 !!! WARNING: HIQ 41 has a net charge of 0.5140 !!! WARNING: SEP 187 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.904173 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -1.621000 45.95900 ymin,ymax (A): 10.27000 56.03500 zmin,zma (A): 10.50600 65.66800 x,y,z range (A): 47.58000 45.76500 55.16200 scale (grids/A): 2.904173 object centre (A): 22.16900 33.15250 38.08700 number of atom coordinates read : 2522 total number of charged atoms : 2383 net assigned charge : 9.039017 assigned positive charge : 383.4510 centred at (gu) : 82.64253 97.09451 89.84074 assigned negative charge : -374.4128 centred at (gu) : 82.17586 96.53529 89.30006 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 176169 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22218 grid for indexing accessible points = 1.400000 m= 88820 mr = 127401 m= 31498 mr = 71463 m= 7244 mr = 24418 m= 912 mr = 5014 m= 44 mr = 532 m= 0 mr = 10 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 1070 time to turn everything in is 1.490000 number of dielectric boundary points 75849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 19056 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.936116 object centre at (A) : 22.16900 33.15250 38.08700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3684901E-02 0.1609375 midg,1,midg; midg,igrid,midg -0.1311191 0.1241449 1,midg,midg; igrid,midg,midg 0.1651653 0.4051660 gauss-seidel spectral radius is 0.9992685 estimated iterations to convergence 292 setup time was (sec) 1.810000 now iterating at: 14:16:16 rms-change max change #iterations 10.13550 439.6423 at 10iterations 5.929543 132.2887 at 20iterations 3.463273 70.81474 at 30iterations 2.019651 45.75061 at 40iterations 1.172900 23.43922 at 50iterations 0.6804562 12.63331 at 60iterations 0.3936563 7.400770 at 70iterations 0.2284905 4.130875 at 80iterations 0.1320169 2.327518 at 90iterations 7.6351620E-02 1.331282 at 100iterations 4.3983735E-02 0.8338022 at 110iterations 2.5432836E-02 0.4745216 at 120iterations 1.4662364E-02 0.2687588 at 130iterations 8.4831202E-03 0.1750584 at 140iterations 4.8848484E-03 8.4419250E-02 at 150iterations 2.8165570E-03 5.3359985E-02 at 160iterations 1.6264413E-03 2.7982235E-02 at 170iterations 9.3762518E-04 1.6830921E-02 at 180iterations finished qdiffx linear iterations at : 14:16:26 total time elapsed so far: 11.99000 # loops : 180 mean,max change (kT/e) : 9.3762518E-04 1.6830921E-02 energy calculations done at 11.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 14:16:26 12.205u 0.188s 0:12.68 97.6% 0+0k 0+0io 0pf+0w