Sun Oct 9 20:46:05 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 20:46:05 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4971 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.5300 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5393286 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): -2.466000 55.94400 ymin,ymax (A): -8.667000 57.34100 zmin,zma (A): -8.834000 52.00700 x,y,z range (A): 58.41000 66.00800 60.84100 scale (grids/A): 0.5393286 object centre (A): 26.73900 24.33700 21.58650 number of atom coordinates read : 4971 total number of charged atoms : 4830 net assigned charge : -2.455938 assigned positive charge : 763.8841 centred at (gu) : 89.81335 89.29709 89.61608 assigned negative charge : -766.3456 centred at (gu) : 89.85943 89.33856 89.67720 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9200 nv = 96 ne = 84 npr = 101864 no. pairs analyzed = 101864 no. exposed pairs = 5615 no. arc points = 38734 no. surface atoms = 1923 nbur = 3048 mkacc time = 0.2300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 423 mr = 5282 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3934 ## 466 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 12371 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6020093E-10 -6.1019073E-10 midg,1,midg; midg,igrid,midg 2.9320682E-10 -4.1489862E-10 1,midg,midg; igrid,midg,midg 2.9872871E-10 -5.1177773E-10 gauss-seidel spectral radius is 0.9824194 estimated iterations to convergence 62 setup time was (sec) 0.6700000 now iterating at: 20:46:06 rms-change max change #iterations 0.1003071 14.58160 at 10iterations 1.1535731E-02 1.770802 at 20iterations 3.9616679E-03 0.6751442 at 30iterations 1.6887750E-03 0.2873077 at 40iterations 7.3072466E-04 0.1221237 at 50iterations finished qdiffx linear iterations at : 20:46:08 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 7.3072466E-04 0.1221237 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 20:46:09 3.315u 0.159s 0:03.75 92.2% 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 20:46:09 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4971 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.5300 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.617986 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): -2.466000 55.94400 ymin,ymax (A): -8.667000 57.34100 zmin,zma (A): -8.834000 52.00700 x,y,z range (A): 58.41000 66.00800 60.84100 scale (grids/A): 1.617986 object centre (A): 26.73900 24.33700 21.58650 number of atom coordinates read : 4971 total number of charged atoms : 4830 net assigned charge : -2.455938 assigned positive charge : 763.8841 centred at (gu) : 89.43853 87.88997 88.84673 assigned negative charge : -766.3456 centred at (gu) : 89.57856 88.01548 89.03179 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 103967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38734 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 34338 mr = 75320 m= 3755 mr = 24559 m= 98 mr = 1883 m= 0 mr = 6 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 492 time to turn everything in is 0.6900000 number of dielectric boundary points 40390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 426 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 36859 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) : 0.5393286 object centre at (A) : 26.73900 24.33700 21.58650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2743500E-02 -1.9427296E-02 midg,1,midg; midg,igrid,midg -1.5754616E-02 -2.3043247E-02 1,midg,midg; igrid,midg,midg 2.3081712E-03 -1.2337539E-02 gauss-seidel spectral radius is 0.9983370 estimated iterations to convergence 195 setup time was (sec) 0.9800000 now iterating at: 20:46:10 rms-change max change #iterations 4.506911 187.3384 at 10iterations 1.953930 67.94390 at 20iterations 0.8507506 27.59657 at 30iterations 0.3703990 11.25102 at 40iterations 0.1619806 4.842794 at 50iterations 7.1521230E-02 2.310396 at 60iterations 3.2228082E-02 1.093777 at 70iterations 1.5585191E-02 0.5382080 at 80iterations 8.4228860E-03 0.2965088 at 90iterations 5.1547959E-03 0.1819229 at 100iterations 3.4742502E-03 0.1164322 at 110iterations 2.4761758E-03 8.2733154E-02 at 120iterations finished qdiffx linear iterations at : 20:46:16 total time elapsed so far: 6.990000 # loops : 120 mean,max change (kT/e) : 2.4761758E-03 8.2733154E-02 energy calculations done at 6.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 20:46:17 7.151u 0.221s 0:07.67 96.0% 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 20:46:17 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4971 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.5300 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.426979 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): -2.466000 55.94400 ymin,ymax (A): -8.667000 57.34100 zmin,zma (A): -8.834000 52.00700 x,y,z range (A): 58.41000 66.00800 60.84100 scale (grids/A): 2.426979 object centre (A): 26.73900 24.33700 21.58650 number of atom coordinates read : 4971 total number of charged atoms : 4830 net assigned charge : -2.455938 assigned positive charge : 763.8841 centred at (gu) : 89.15749 86.83440 88.26991 assigned negative charge : -766.3456 centred at (gu) : 89.36781 87.02320 88.54764 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 241987 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38734 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 117489 mr = 183601 m= 35480 mr = 95535 m= 5999 mr = 27195 m= 426 mr = 4010 m= 4 mr = 172 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 1690 time to turn everything in is 1.660000 number of dielectric boundary points 90872 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 38570 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) : 1.617986 object centre at (A) : 26.73900 24.33700 21.58650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1881230 -0.4716090 midg,1,midg; midg,igrid,midg -0.3984612 -0.3884460 1,midg,midg; igrid,midg,midg 9.0730600E-02 -0.1672492 gauss-seidel spectral radius is 0.9992220 estimated iterations to convergence 283 setup time was (sec) 1.950000 now iterating at: 20:46:19 rms-change max change #iterations 11.64949 290.1921 at 10iterations 6.773649 145.5207 at 20iterations 3.920981 79.49503 at 30iterations 2.253532 38.84992 at 40iterations 1.295898 26.74229 at 50iterations 0.7423944 12.66083 at 60iterations 0.4228673 7.884424 at 70iterations 0.2420399 4.019112 at 80iterations 0.1379825 2.522106 at 90iterations 7.8656435E-02 1.404327 at 100iterations 4.5167159E-02 0.8050766 at 110iterations 2.6055194E-02 0.4627304 at 120iterations 1.5283324E-02 0.2732162 at 130iterations 9.2265783E-03 0.1686554 at 140iterations 5.8037587E-03 0.1175537 at 150iterations 3.8794086E-03 8.5279465E-02 at 160iterations 2.7829097E-03 5.9463501E-02 at 170iterations 2.1063332E-03 4.7630310E-02 at 180iterations finished qdiffx linear iterations at : 20:46:28 total time elapsed so far: 11.64000 # loops : 180 mean,max change (kT/e) : 2.1063332E-03 4.7630310E-02 energy calculations done at 11.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 20:46:29 11.810u 0.172s 0:12.25 97.7% 0+0k 0+0io 0pf+0w