Sat Oct 8 11:39:09 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 11:39:09 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3378 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: HIR 238 has a net charge of 0.5140 !!! WARNING: ZN4 461 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6522895 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): -22.52700 32.05000 ymin,ymax (A): -1.731000 50.81000 zmin,zma (A): 11.11600 59.76800 x,y,z range (A): 54.57700 52.54100 48.65200 scale (grids/A): 0.6522895 object centre (A): 4.761499 24.53950 35.44200 number of atom coordinates read : 3378 total number of charged atoms : 3254 net assigned charge : -3.985969 assigned positive charge : 520.0334 centred at (gu) : 90.57336 90.96461 89.42836 assigned negative charge : -524.0203 centred at (gu) : 90.60332 90.80079 89.56013 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 9501 nv = 96 ne = 84 npr = 70634 no. pairs analyzed = 70634 no. exposed pairs = 3667 no. arc points = 25042 no. surface atoms = 1271 nbur = 2107 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 533 mr = 5802 m= 4 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2500000 number of dielectric boundary points 4130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2436 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 11533 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2375037E-08 -3.3574658E-08 midg,1,midg; midg,igrid,midg -3.6795310E-08 3.2763872E-08 1,midg,midg; igrid,midg,midg -1.9457884E-09 -1.7183607E-08 gauss-seidel spectral radius is 0.9878770 estimated iterations to convergence 74 setup time was (sec) 0.4600000 now iterating at: 11:39:10 rms-change max change #iterations 0.1930806 25.11224 at 10iterations 1.9969536E-02 2.567787 at 20iterations 2.1047147E-03 0.2494698 at 30iterations 2.2113445E-04 2.5970697E-02 at 40iterations 2.3280185E-05 2.7055740E-03 at 50iterations finished qdiffx linear iterations at : 11:39:13 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 2.3280185E-05 2.7055740E-03 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 11:39:13 3.742u 0.220s 0:04.46 88.7% 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 11:39:13 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3378 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: HIR 238 has a net charge of 0.5140 !!! WARNING: ZN4 461 has a net charge of 1.4000 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: 1.956868 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): -22.52700 32.05000 ymin,ymax (A): -1.731000 50.81000 zmin,zma (A): 11.11600 59.76800 x,y,z range (A): 54.57700 52.54100 48.65200 scale (grids/A): 1.956868 object centre (A): 4.761499 24.53950 35.44200 number of atom coordinates read : 3378 total number of charged atoms : 3254 net assigned charge : -3.985969 assigned positive charge : 520.0334 centred at (gu) : 91.71920 92.89285 88.28412 assigned negative charge : -524.0203 centred at (gu) : 91.80935 92.40155 88.68000 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 103084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25042 grid for indexing accessible points = 1.400000 m= 40604 mr = 76423 m= 6768 mr = 31920 m= 418 mr = 4604 m= 10 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 283 time to turn everything in is 0.5000000 number of dielectric boundary points 37787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 25683 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) : 0.6522895 object centre at (A) : 4.761499 24.53950 35.44200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2968003E-03 -7.5688459E-02 midg,1,midg; midg,igrid,midg -4.7471929E-02 3.2779839E-02 1,midg,midg; igrid,midg,midg -1.6108875E-03 -1.9028530E-02 gauss-seidel spectral radius is 0.9987593 estimated iterations to convergence 225 setup time was (sec) 0.7400000 now iterating at: 11:39:14 rms-change max change #iterations 5.285012 192.1125 at 10iterations 2.563779 74.36388 at 20iterations 1.246827 34.55651 at 30iterations 0.6063775 15.16132 at 40iterations 0.2944360 7.574921 at 50iterations 0.1432965 3.762838 at 60iterations 6.9678426E-02 1.763870 at 70iterations 3.3878874E-02 0.8639994 at 80iterations 1.6432801E-02 0.4168943 at 90iterations 8.0196420E-03 0.2077780 at 100iterations 3.8883716E-03 0.1014233 at 110iterations 1.9002237E-03 4.7500610E-02 at 120iterations finished qdiffx linear iterations at : 11:39:22 total time elapsed so far: 8.410000 # loops : 120 mean,max change (kT/e) : 1.9002237E-03 4.7500610E-02 energy calculations done at 8.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.540000 DelPhi exited at 11:39:23 8.540u 0.244s 0:09.12 96.2% 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 Sat Oct 8 2011 at 11:39:23 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3378 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: HIR 238 has a net charge of 0.5140 !!! WARNING: ZN4 461 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.935302 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): -22.52700 32.05000 ymin,ymax (A): -1.731000 50.81000 zmin,zma (A): 11.11600 59.76800 x,y,z range (A): 54.57700 52.54100 48.65200 scale (grids/A): 2.935302 object centre (A): 4.761499 24.53950 35.44200 number of atom coordinates read : 3378 total number of charged atoms : 3254 net assigned charge : -3.985969 assigned positive charge : 520.0334 centred at (gu) : 92.57848 94.33904 87.42586 assigned negative charge : -524.0203 centred at (gu) : 92.71384 93.60229 88.01978 start vw surface at 0.1000000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 238223 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25042 grid for indexing accessible points = 1.400000 m= 129082 mr = 183146 m= 50447 mr = 109990 m= 12475 mr = 42805 m= 1941 mr = 9814 m= 118 mr = 1298 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.8000001 no. cavity mid-points inaccessible to solvent = 1068 time to turn everything in is 1.360000 number of dielectric boundary points 85204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 26032 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) : 1.956868 object centre at (A) : 4.761499 24.53950 35.44200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7747690E-02 -0.8282229 midg,1,midg; midg,igrid,midg -0.4352296 0.3544025 1,midg,midg; igrid,midg,midg -0.1352539 -0.1635909 gauss-seidel spectral radius is 0.9992930 estimated iterations to convergence 297 setup time was (sec) 1.640000 now iterating at: 11:39:25 rms-change max change #iterations 12.13328 495.6887 at 10iterations 7.183118 155.5755 at 20iterations 4.224299 83.17216 at 30iterations 2.485976 43.02356 at 40iterations 1.456280 22.59097 at 50iterations 0.8525242 13.84160 at 60iterations 0.4982467 7.493990 at 70iterations 0.2907791 4.298966 at 80iterations 0.1700277 2.858568 at 90iterations 9.9180616E-02 1.485599 at 100iterations 5.7876322E-02 0.9465561 at 110iterations 3.3742771E-02 0.5216904 at 120iterations 1.9657392E-02 0.3139648 at 130iterations 1.1453429E-02 0.1732292 at 140iterations 6.6656261E-03 9.9861145E-02 at 150iterations 3.8848436E-03 6.0558319E-02 at 160iterations 2.2658694E-03 3.5426140E-02 at 170iterations 1.3195403E-03 2.0860910E-02 at 180iterations finished qdiffx linear iterations at : 11:39:38 total time elapsed so far: 14.78000 # loops : 180 mean,max change (kT/e) : 1.3195403E-03 2.0860910E-02 energy calculations done at 14.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.91000 DelPhi exited at 11:39:38 14.916u 0.268s 0:15.49 97.9% 0+0k 0+0io 0pf+0w