Mon Oct 10 22:55:23 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 Mon Oct 10 2011 at 22:55:23 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2645 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 0.6298321 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): -20.36000 31.15200 ymin,ymax (A): 20.20400 76.72700 zmin,zma (A): 9.452000 52.01700 x,y,z range (A): 51.51200 56.52299 42.56500 scale (grids/A): 0.6298321 object centre (A): 5.396001 48.46550 30.73450 number of atom coordinates read : 2645 total number of charged atoms : 2498 net assigned charge : 2.406015 assigned positive charge : 397.8328 centred at (gu) : 91.70656 88.56892 89.93204 assigned negative charge : -395.4274 centred at (gu) : 91.65005 88.90748 90.13335 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6910 nv = 96 ne = 84 npr = 53940 no. pairs analyzed = 53940 no. exposed pairs = 3085 no. arc points = 21497 no. surface atoms = 1046 nbur = 1599 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 351 mr = 3956 m= 0 mr = 40 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2059 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8438 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9955868E-08 -1.6071203E-08 midg,1,midg; midg,igrid,midg 4.2881858E-08 -2.1379387E-08 1,midg,midg; igrid,midg,midg -2.0324327E-09 1.0306993E-08 gauss-seidel spectral radius is 0.9869413 estimated iterations to convergence 72 setup time was (sec) 0.5800000 now iterating at: 22:55:24 rms-change max change #iterations 0.1396994 25.35896 at 10iterations 1.4176846E-02 2.518364 at 20iterations 1.7987567E-03 0.3717880 at 30iterations 4.3545436E-04 0.1016731 at 40iterations 1.3066335E-04 3.1425476E-02 at 50iterations finished qdiffx linear iterations at : 22:55:27 total time elapsed so far: 3.650000 # loops : 50 mean,max change (kT/e) : 1.3066335E-04 3.1425476E-02 energy calculations done at 3.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.830000 DelPhi exited at 22:55:28 3.833u 0.391s 0:04.79 88.1% 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 Mon Oct 10 2011 at 22:55:28 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2645 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 1.889496 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): -20.36000 31.15200 ymin,ymax (A): 20.20400 76.72700 zmin,zma (A): 9.452000 52.01700 x,y,z range (A): 51.51200 56.52299 42.56500 scale (grids/A): 1.889496 object centre (A): 5.396001 48.46550 30.73450 number of atom coordinates read : 2645 total number of charged atoms : 2498 net assigned charge : 2.406015 assigned positive charge : 397.8328 centred at (gu) : 95.11937 85.70649 89.79575 assigned negative charge : -395.4274 centred at (gu) : 94.95000 86.72211 90.39970 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 75433 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21497 grid for indexing accessible points = 1.400000 m= 26721 mr = 53449 m= 4167 mr = 20191 m= 201 mr = 2718 m= 2 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2236 time to turn everything in is 0.5700000 number of dielectric boundary points 30095 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19653 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) : 0.6298321 object centre at (A) : 5.396001 48.46550 30.73450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9999280E-02 8.2685769E-04 midg,1,midg; midg,igrid,midg 1.9031936E-02 -6.1722070E-02 1,midg,midg; igrid,midg,midg -5.6813792E-03 -3.6290616E-03 gauss-seidel spectral radius is 0.9986098 estimated iterations to convergence 213 setup time was (sec) 0.8400000 now iterating at: 22:55:29 rms-change max change #iterations 4.208724 174.6483 at 10iterations 1.946821 67.97315 at 20iterations 0.9056027 26.28807 at 30iterations 0.4219255 13.34442 at 40iterations 0.1962812 5.848335 at 50iterations 9.1535203E-02 3.296223 at 60iterations 4.2633425E-02 1.424316 at 70iterations 1.9988082E-02 0.6702614 at 80iterations 9.4304178E-03 0.2848015 at 90iterations 4.5094672E-03 0.1678963 at 100iterations 2.2152886E-03 7.4924469E-02 at 110iterations 1.1358687E-03 4.4895172E-02 at 120iterations finished qdiffx linear iterations at : 22:55:37 total time elapsed so far: 8.390000 # loops : 120 mean,max change (kT/e) : 1.1358687E-03 4.4895172E-02 energy calculations done at 8.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.560000 DelPhi exited at 22:55:37 8.567u 0.445s 0:09.51 94.6% 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 Mon Oct 10 2011 at 22:55:37 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2645 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 2.834245 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): -20.36000 31.15200 ymin,ymax (A): 20.20400 76.72700 zmin,zma (A): 9.452000 52.01700 x,y,z range (A): 51.51200 56.52299 42.56500 scale (grids/A): 2.834245 object centre (A): 5.396001 48.46550 30.73450 number of atom coordinates read : 2645 total number of charged atoms : 2498 net assigned charge : 2.406015 assigned positive charge : 397.8328 centred at (gu) : 97.67903 83.55960 89.69360 assigned negative charge : -395.4274 centred at (gu) : 97.42486 85.08314 90.59946 start vw surface at 0.1300000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 174410 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21497 grid for indexing accessible points = 1.400000 m= 88135 mr = 129234 m= 31296 mr = 73271 m= 7593 mr = 25489 m= 1003 mr = 6020 m= 52 mr = 678 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 7629 time to turn everything in is 1.520000 number of dielectric boundary points 67778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 19984 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) : 1.889496 object centre at (A) : 5.396001 48.46550 30.73450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2921942 5.6615137E-02 midg,1,midg; midg,igrid,midg -0.2658522 -0.6028858 1,midg,midg; igrid,midg,midg -0.1180166 -0.1197443 gauss-seidel spectral radius is 0.9992462 estimated iterations to convergence 287 setup time was (sec) 1.830000 now iterating at: 22:55:40 rms-change max change #iterations 9.794564 348.7337 at 10iterations 5.644953 137.4377 at 20iterations 3.251957 63.51704 at 30iterations 1.867979 42.91924 at 40iterations 1.070490 19.98372 at 50iterations 0.6130915 12.85321 at 60iterations 0.3501831 7.081572 at 70iterations 0.2005877 3.793488 at 80iterations 0.1145382 2.230667 at 90iterations 6.5636188E-02 1.181854 at 100iterations 3.7552424E-02 0.6888351 at 110iterations 2.1464689E-02 0.3849812 at 120iterations 1.2330873E-02 0.2172852 at 130iterations 7.0982124E-03 0.1300621 at 140iterations 4.1249651E-03 8.2504272E-02 at 150iterations 2.4184319E-03 5.1477432E-02 at 160iterations 1.4567110E-03 3.6434174E-02 at 170iterations 9.1443630E-04 2.1640778E-02 at 180iterations finished qdiffx linear iterations at : 22:55:53 total time elapsed so far: 14.61000 # loops : 180 mean,max change (kT/e) : 9.1443630E-04 2.1640778E-02 energy calculations done at 14.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.78000 DelPhi exited at 22:55:53 14.781u 0.464s 0:15.79 96.5% 0+0k 0+0io 0pf+0w