Sun Oct 9 11:53:57 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 11:53:57 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2687 !!! WARNING: HIR 202 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6772825 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): 51.10200 103.6650 ymin,ymax (A): 5.018000 55.91400 zmin,zma (A): 36.05300 88.58000 x,y,z range (A): 52.56300 50.89600 52.52700 scale (grids/A): 0.6772825 object centre (A): 77.38350 30.46600 62.31650 number of atom coordinates read : 2687 total number of charged atoms : 2546 net assigned charge : 0.5140090 assigned positive charge : 386.0843 centred at (gu) : 89.29704 90.00175 92.11716 assigned negative charge : -385.5718 centred at (gu) : 89.47112 90.08864 92.02880 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8943 nv = 96 ne = 84 npr = 53147 no. pairs analyzed = 53147 no. exposed pairs = 3619 no. arc points = 25833 no. surface atoms = 1222 nbur = 1465 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 640 mr = 4752 m= 3 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2000000 number of dielectric boundary points 4709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2143 ## 119 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9719 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6678950E-08 4.2771774E-08 midg,1,midg; midg,igrid,midg 2.7008339E-08 -2.5347687E-08 1,midg,midg; igrid,midg,midg 6.0860216E-08 -4.5234319E-08 gauss-seidel spectral radius is 0.9887289 estimated iterations to convergence 77 setup time was (sec) 0.3800000 now iterating at: 11:53:58 rms-change max change #iterations 0.1892846 26.05595 at 10iterations 2.1690454E-02 2.913873 at 20iterations 2.6662506E-03 0.3391094 at 30iterations 4.7597120E-04 7.1985245E-02 at 40iterations 1.4022712E-04 2.4433136E-02 at 50iterations finished qdiffx linear iterations at : 11:54:01 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.4022712E-04 2.4433136E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 11:54:01 3.364u 0.178s 0:03.82 92.4% 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 11:54:01 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2687 !!! WARNING: HIR 202 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.031847 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): 51.10200 103.6650 ymin,ymax (A): 5.018000 55.91400 zmin,zma (A): 36.05300 88.58000 x,y,z range (A): 52.56300 50.89600 52.52700 scale (grids/A): 2.031847 object centre (A): 77.38350 30.46600 62.31650 number of atom coordinates read : 2687 total number of charged atoms : 2546 net assigned charge : 0.5140090 assigned positive charge : 386.0843 centred at (gu) : 87.89061 90.00447 96.35078 assigned negative charge : -385.5718 centred at (gu) : 88.41328 90.26590 96.08633 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 93766 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25833 grid for indexing accessible points = 1.400000 m= 37396 mr = 63538 m= 8164 mr = 27425 m= 786 mr = 5533 m= 10 mr = 354 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 428 time to turn everything in is 0.4500000 number of dielectric boundary points 43273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 20189 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) : 0.6772825 object centre at (A) : 77.38350 30.46600 62.31650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5567778E-02 7.8429282E-02 midg,1,midg; midg,igrid,midg 2.0355826E-02 -1.1480788E-02 1,midg,midg; igrid,midg,midg 3.4170978E-02 -5.1605910E-02 gauss-seidel spectral radius is 0.9988284 estimated iterations to convergence 231 setup time was (sec) 0.6800000 now iterating at: 11:54:02 rms-change max change #iterations 4.832350 204.5322 at 10iterations 2.392046 71.63790 at 20iterations 1.177548 33.60363 at 30iterations 0.5851951 17.65909 at 40iterations 0.2909684 8.890625 at 50iterations 0.1437145 4.271131 at 60iterations 7.1382470E-02 1.995859 at 70iterations 3.5425153E-02 0.9765778 at 80iterations 1.7639222E-02 0.4773254 at 90iterations 8.7870797E-03 0.2543001 at 100iterations 4.4095805E-03 0.1189938 at 110iterations 2.2393949E-03 6.9255829E-02 at 120iterations finished qdiffx linear iterations at : 11:54:09 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 2.2393949E-03 6.9255829E-02 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 11:54:10 8.006u 0.196s 0:08.53 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 11:54:10 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2687 !!! WARNING: HIR 202 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.047771 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): 51.10200 103.6650 ymin,ymax (A): 5.018000 55.91400 zmin,zma (A): 36.05300 88.58000 x,y,z range (A): 52.56300 50.89600 52.52700 scale (grids/A): 3.047771 object centre (A): 77.38350 30.46600 62.31650 number of atom coordinates read : 2687 total number of charged atoms : 2546 net assigned charge : 0.5140090 assigned positive charge : 386.0843 centred at (gu) : 86.83564 90.00653 99.52614 assigned negative charge : -385.5718 centred at (gu) : 87.61978 90.39891 99.12946 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 216321 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25833 grid for indexing accessible points = 1.400000 m= 113173 mr = 154247 m= 49334 mr = 91671 m= 15750 mr = 39869 m= 3307 mr = 12267 m= 277 mr = 2425 m= 6 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 1542 time to turn everything in is 1.250000 number of dielectric boundary points 97547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 20368 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) : 2.031847 object centre at (A) : 77.38350 30.46600 62.31650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1032056 0.9248146 midg,1,midg; midg,igrid,midg 0.1941091 -0.3586732 1,midg,midg; igrid,midg,midg 0.2802271 -0.4570467 gauss-seidel spectral radius is 0.9993284 estimated iterations to convergence 304 setup time was (sec) 1.490000 now iterating at: 11:54:11 rms-change max change #iterations 11.17878 492.0339 at 10iterations 6.752917 157.0211 at 20iterations 4.071749 91.03395 at 30iterations 2.443830 47.45883 at 40iterations 1.462191 31.67434 at 50iterations 0.8731056 14.10340 at 60iterations 0.5191907 9.215440 at 70iterations 0.3083494 4.744526 at 80iterations 0.1830245 3.456318 at 90iterations 0.1087023 1.680824 at 100iterations 6.4250372E-02 1.043798 at 110iterations 3.8108688E-02 0.6104469 at 120iterations 2.2538975E-02 0.3737612 at 130iterations 1.3381061E-02 0.2176089 at 140iterations 7.9518463E-03 0.1406612 at 150iterations 4.7611166E-03 7.4840546E-02 at 160iterations 2.8735192E-03 5.4241180E-02 at 170iterations 1.7652046E-03 3.1777382E-02 at 180iterations finished qdiffx linear iterations at : 11:54:23 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 1.7652046E-03 3.1777382E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.24000 DelPhi exited at 11:54:24 13.238u 0.200s 0:13.70 98.0% 0+0k 0+0io 0pf+0w