Sat Oct 8 11:39:02 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 Sat Oct 8 2011 at 11:39:03 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3130 !!! WARNING: HIR 281 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5661848 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): 5.916000 67.18200 ymin,ymax (A): -8.260000 38.79700 zmin,zma (A): -24.46600 38.41100 x,y,z range (A): 61.26600 47.05700 62.87700 scale (grids/A): 0.5661848 object centre (A): 36.54900 15.26850 6.972502 number of atom coordinates read : 3130 total number of charged atoms : 2983 net assigned charge : -9.985968 assigned positive charge : 463.3396 centred at (gu) : 87.98566 90.46049 91.81099 assigned negative charge : -473.3266 centred at (gu) : 87.88700 90.53993 91.90513 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6561 nv = 96 ne = 84 npr = 64270 no. pairs analyzed = 64270 no. exposed pairs = 4018 no. arc points = 27108 no. surface atoms = 1372 nbur = 1758 mkacc time = 0.1100000 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 = 1.512000 m= 305 mr = 3468 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2676 ## 269 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 8464 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4659915E-11 -4.0741135E-09 midg,1,midg; midg,igrid,midg -1.0669976E-10 -2.6978355E-09 1,midg,midg; igrid,midg,midg -4.3914992E-09 8.0189404E-11 gauss-seidel spectral radius is 0.9839156 estimated iterations to convergence 65 setup time was (sec) 0.4900000 now iterating at: 11:39:03 rms-change max change #iterations 9.1271378E-02 14.97669 at 10iterations 7.6667434E-03 1.232738 at 20iterations 2.1395811E-03 0.3963394 at 30iterations 1.0493794E-03 0.1948719 at 40iterations 5.2730617E-04 9.6851349E-02 at 50iterations finished qdiffx linear iterations at : 11:39:07 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 5.2730617E-04 9.6851349E-02 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 11:39:07 4.008u 0.229s 0:04.67 90.3% 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 Sat Oct 8 2011 at 11:39:07 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3130 !!! WARNING: HIR 281 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.698554 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): 5.916000 67.18200 ymin,ymax (A): -8.260000 38.79700 zmin,zma (A): -24.46600 38.41100 x,y,z range (A): 61.26600 47.05700 62.87700 scale (grids/A): 1.698554 object centre (A): 36.54900 15.26850 6.972502 number of atom coordinates read : 3130 total number of charged atoms : 2983 net assigned charge : -9.985968 assigned positive charge : 463.3396 centred at (gu) : 83.95603 91.38023 95.43248 assigned negative charge : -473.3266 centred at (gu) : 83.66053 91.61922 95.71471 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 72423 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27108 grid for indexing accessible points = 1.400000 m= 23575 mr = 50025 m= 2899 mr = 16394 m= 96 mr = 1570 m= 3 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 574 time to turn everything in is 0.3800000 number of dielectric boundary points 30998 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 23091 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) : 0.5661848 object centre at (A) : 36.54900 15.26850 6.972502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0471118E-03 -2.7052328E-02 midg,1,midg; midg,igrid,midg -8.9249695E-03 -1.4458675E-02 1,midg,midg; igrid,midg,midg -1.8725667E-02 -6.8765962E-03 gauss-seidel spectral radius is 0.9983331 estimated iterations to convergence 194 setup time was (sec) 0.6300000 now iterating at: 11:39:08 rms-change max change #iterations 3.731323 139.5199 at 10iterations 1.611327 59.59457 at 20iterations 0.6975859 27.16531 at 30iterations 0.3031875 10.46981 at 40iterations 0.1311940 4.469555 at 50iterations 5.7234187E-02 1.878350 at 60iterations 2.5350004E-02 0.8226087 at 70iterations 1.1581348E-02 0.4473610 at 80iterations 5.8113299E-03 0.2174225 at 90iterations 3.4141983E-03 0.1352158 at 100iterations 2.3410472E-03 9.6639633E-02 at 110iterations 1.7500274E-03 6.5847397E-02 at 120iterations finished qdiffx linear iterations at : 11:39:16 total time elapsed so far: 8.830000 # loops : 120 mean,max change (kT/e) : 1.7500274E-03 6.5847397E-02 energy calculations done at 8.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.960000 DelPhi exited at 11:39:17 8.964u 0.272s 0:09.66 95.5% 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 Sat Oct 8 2011 at 11:39:17 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3130 !!! WARNING: HIR 281 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.547831 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): 5.916000 67.18200 ymin,ymax (A): -8.260000 38.79700 zmin,zma (A): -24.46600 38.41100 x,y,z range (A): 61.26600 47.05700 62.87700 scale (grids/A): 2.547831 object centre (A): 36.54900 15.26850 6.972502 number of atom coordinates read : 3130 total number of charged atoms : 2983 net assigned charge : -9.985968 assigned positive charge : 463.3396 centred at (gu) : 80.93394 92.07027 98.14845 assigned negative charge : -473.3266 centred at (gu) : 80.49050 92.42867 98.57206 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 168352 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27108 grid for indexing accessible points = 1.400000 m= 79906 mr = 122221 m= 24805 mr = 63862 m= 4705 mr = 18749 m= 404 mr = 3232 m= 8 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 2103 time to turn everything in is 0.9600000 number of dielectric boundary points 69922 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 23846 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) : 1.698554 object centre at (A) : 36.54900 15.26850 6.972502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1123978 -0.2183937 midg,1,midg; midg,igrid,midg -0.1753675 -0.1664180 1,midg,midg; igrid,midg,midg -0.4200280 -8.7423421E-02 gauss-seidel spectral radius is 0.9991848 estimated iterations to convergence 277 setup time was (sec) 1.230000 now iterating at: 11:39:19 rms-change max change #iterations 9.542154 327.9050 at 10iterations 5.471793 142.5402 at 20iterations 3.130353 79.07952 at 30iterations 1.784064 40.43307 at 40iterations 1.008144 21.17579 at 50iterations 0.5693721 11.35402 at 60iterations 0.3210261 6.138195 at 70iterations 0.1808512 4.060326 at 80iterations 0.1015446 1.965187 at 90iterations 5.7134155E-02 1.209034 at 100iterations 3.2169048E-02 0.6511040 at 110iterations 1.8133027E-02 0.3707142 at 120iterations 1.0344443E-02 0.1948414 at 130iterations 6.0036257E-03 0.1225796 at 140iterations 3.6180425E-03 7.3196411E-02 at 150iterations 2.3359377E-03 5.2833557E-02 at 160iterations 1.6456442E-03 3.6684036E-02 at 170iterations 1.2612046E-03 2.7961731E-02 at 180iterations finished qdiffx linear iterations at : 11:39:32 total time elapsed so far: 14.50000 # loops : 180 mean,max change (kT/e) : 1.2612046E-03 2.7961731E-02 energy calculations done at 14.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.63000 DelPhi exited at 11:39:33 14.630u 0.304s 0:15.62 95.5% 0+0k 0+0io 0pf+0w