Sun Oct 9 17:05:03 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 17:05:03 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4988 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5543704 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): 3.308000 64.65600 ymin,ymax (A): -9.105000 53.43000 zmin,zma (A): -2.311000 61.90600 x,y,z range (A): 61.34800 62.53500 64.21700 scale (grids/A): 0.5543704 object centre (A): 33.98200 22.16250 29.79750 number of atom coordinates read : 4988 total number of charged atoms : 4844 net assigned charge : 0.2540475 assigned positive charge : 769.0313 centred at (gu) : 88.48225 89.36141 89.32713 assigned negative charge : -768.7826 centred at (gu) : 88.36303 89.40044 89.31390 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 10024 nv = 96 ne = 84 npr = 101199 no. pairs analyzed = 101199 no. exposed pairs = 5754 no. arc points = 39329 no. surface atoms = 1962 nbur = 3026 mkacc time = 0.1800000 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= 450 mr = 5767 m= 0 mr = 18 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4043 ## 430 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 13151 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8354036E-10 2.1821801E-10 midg,1,midg; midg,igrid,midg 7.7045198E-10 -4.7788912E-10 1,midg,midg; igrid,midg,midg -2.6864866E-09 1.2969797E-09 gauss-seidel spectral radius is 0.9833646 estimated iterations to convergence 64 setup time was (sec) 0.5200000 now iterating at: 17:05:03 rms-change max change #iterations 0.1115754 14.17857 at 10iterations 1.2246982E-02 1.611755 at 20iterations 4.4014775E-03 0.6457596 at 30iterations 1.9806356E-03 0.2938538 at 40iterations 9.0025336E-04 0.1339417 at 50iterations finished qdiffx linear iterations at : 17:05:06 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 9.0025336E-04 0.1339417 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 17:05:07 3.561u 0.185s 0:04.03 92.8% 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 17:05:07 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4988 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.663111 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): 3.308000 64.65600 ymin,ymax (A): -9.105000 53.43000 zmin,zma (A): -2.311000 61.90600 x,y,z range (A): 61.34800 62.53500 64.21700 scale (grids/A): 1.663111 object centre (A): 33.98200 22.16250 29.79750 number of atom coordinates read : 4988 total number of charged atoms : 4844 net assigned charge : 0.2540475 assigned positive charge : 769.0313 centred at (gu) : 85.44540 88.08302 87.97986 assigned negative charge : -768.7826 centred at (gu) : 85.08900 88.20105 87.94144 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 112048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39329 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 38083 mr = 81549 m= 4354 mr = 27322 m= 151 mr = 2289 m= 0 mr = 38 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 43438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 371 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 37322 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) : 0.5543704 object centre at (A) : 33.98200 22.16250 29.79750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3887513E-02 -2.7774112E-02 midg,1,midg; midg,igrid,midg 2.0222789E-02 1.0790796E-02 1,midg,midg; igrid,midg,midg -1.8787963E-02 2.6932299E-02 gauss-seidel spectral radius is 0.9984378 estimated iterations to convergence 201 setup time was (sec) 0.7500000 now iterating at: 17:05:08 rms-change max change #iterations 4.831135 159.5198 at 10iterations 2.141753 68.50056 at 20iterations 0.9555743 26.69762 at 30iterations 0.4268439 13.02464 at 40iterations 0.1903534 5.571339 at 50iterations 8.6102217E-02 2.466286 at 60iterations 3.9617401E-02 1.119804 at 70iterations 1.9079007E-02 0.5439758 at 80iterations 1.0105822E-02 0.3401794 at 90iterations 6.0690539E-03 0.1939163 at 100iterations 4.0788236E-03 0.1278839 at 110iterations 2.9095416E-03 8.9309692E-02 at 120iterations finished qdiffx linear iterations at : 17:05:15 total time elapsed so far: 8.020000 # loops : 120 mean,max change (kT/e) : 2.9095416E-03 8.9309692E-02 energy calculations done at 8.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 17:05:15 8.141u 0.224s 0:08.64 96.7% 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 Sun Oct 9 2011 at 17:05:15 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4988 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.494667 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): 3.308000 64.65600 ymin,ymax (A): -9.105000 53.43000 zmin,zma (A): -2.311000 61.90600 x,y,z range (A): 61.34800 62.53500 64.21700 scale (grids/A): 2.494667 object centre (A): 33.98200 22.16250 29.79750 number of atom coordinates read : 4988 total number of charged atoms : 4844 net assigned charge : 0.2540475 assigned positive charge : 769.0313 centred at (gu) : 83.16779 87.12423 86.96948 assigned negative charge : -768.7826 centred at (gu) : 82.63356 87.30134 86.91215 start vw surface at 0.1200000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 260908 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39329 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 130252 mr = 198503 m= 39739 mr = 106122 m= 6964 mr = 30634 m= 612 mr = 4756 m= 23 mr = 345 m= 0 mr = 3 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 98135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 38709 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) : 1.663111 object centre at (A) : 33.98200 22.16250 29.79750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3392516 -0.6589078 midg,1,midg; midg,igrid,midg 0.1211438 5.1468268E-02 1,midg,midg; igrid,midg,midg -0.4117351 0.3844992 gauss-seidel spectral radius is 0.9992528 estimated iterations to convergence 289 setup time was (sec) 1.600000 now iterating at: 17:05:17 rms-change max change #iterations 12.21406 285.0960 at 10iterations 7.203773 158.8442 at 20iterations 4.214250 78.22731 at 30iterations 2.461184 46.92144 at 40iterations 1.428727 24.65549 at 50iterations 0.8281918 14.48201 at 60iterations 0.4787818 8.208820 at 70iterations 0.2766269 4.322144 at 80iterations 0.1597783 2.733063 at 90iterations 9.2289962E-02 1.651896 at 100iterations 5.3583331E-02 0.8506699 at 110iterations 3.1270131E-02 0.4875591 at 120iterations 1.8520642E-02 0.3110352 at 130iterations 1.1288060E-02 0.1983261 at 140iterations 7.1600960E-03 0.1315155 at 150iterations 4.8483633E-03 9.0835571E-02 at 160iterations 3.5106414E-03 7.1437836E-02 at 170iterations 2.6894745E-03 5.0376892E-02 at 180iterations finished qdiffx linear iterations at : 17:05:29 total time elapsed so far: 13.53000 # loops : 180 mean,max change (kT/e) : 2.6894745E-03 5.0376892E-02 energy calculations done at 13.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.66000 DelPhi exited at 17:05:30 13.662u 0.225s 0:14.16 98.0% 0+0k 0+0io 0pf+0w