Sun Oct 9 12:20:43 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 12:20:43 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 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: 0.6737958 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): -14.27500 38.56000 ymin,ymax (A): -0.1560000 44.71900 zmin,zma (A): -7.104000 43.75900 x,y,z range (A): 52.83500 44.87500 50.86300 scale (grids/A): 0.6737958 object centre (A): 12.14250 22.28150 18.32750 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500025 assigned positive charge : 373.0132 centred at (gu) : 90.64111 91.11273 89.99398 assigned negative charge : -369.5135 centred at (gu) : 90.82992 91.17771 89.96187 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7222 nv = 96 ne = 84 npr = 48222 no. pairs analyzed = 48222 no. exposed pairs = 3128 no. arc points = 21210 no. surface atoms = 1052 nbur = 1364 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 461 mr = 3907 m= 4 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.1900000 number of dielectric boundary points 3699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2006 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8466 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8860924E-09 2.1929907E-08 midg,1,midg; midg,igrid,midg 2.4440311E-08 -5.2015072E-09 1,midg,midg; igrid,midg,midg 5.4945026E-08 -4.3295106E-08 gauss-seidel spectral radius is 0.9885617 estimated iterations to convergence 76 setup time was (sec) 0.3900000 now iterating at: 12:20:44 rms-change max change #iterations 0.1815298 28.01503 at 10iterations 2.0366302E-02 2.871431 at 20iterations 2.6860798E-03 0.3691444 at 30iterations 5.3851859E-04 7.9975367E-02 at 40iterations 1.6792136E-04 2.3366928E-02 at 50iterations finished qdiffx linear iterations at : 12:20:47 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.6792136E-04 2.3366928E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 12:20:47 3.445u 0.215s 0:04.02 90.7% 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 12:20:47 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 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: 2.021387 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): -14.27500 38.56000 ymin,ymax (A): -0.1560000 44.71900 zmin,zma (A): -7.104000 43.75900 x,y,z range (A): 52.83500 44.87500 50.86300 scale (grids/A): 2.021387 object centre (A): 12.14250 22.28150 18.32750 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500025 assigned positive charge : 373.0132 centred at (gu) : 91.92295 93.33755 89.98170 assigned negative charge : -369.5135 centred at (gu) : 92.48949 93.53285 89.88551 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76545 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21210 grid for indexing accessible points = 1.400000 m= 28791 mr = 52201 m= 5311 mr = 21222 m= 388 mr = 3438 m= 14 mr = 180 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 860 time to turn everything in is 0.4100000 number of dielectric boundary points 34007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 17989 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) : 0.6737958 object centre at (A) : 12.14250 22.28150 18.32750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2514660E-02 1.5187862E-02 midg,1,midg; midg,igrid,midg 3.3695128E-02 2.2220032E-03 1,midg,midg; igrid,midg,midg 2.1675158E-02 -4.7642399E-02 gauss-seidel spectral radius is 0.9987666 estimated iterations to convergence 225 setup time was (sec) 0.6300000 now iterating at: 12:20:48 rms-change max change #iterations 4.683487 236.2536 at 10iterations 2.266996 83.38042 at 20iterations 1.099743 34.81530 at 30iterations 0.5369321 16.46917 at 40iterations 0.2600863 8.845657 at 50iterations 0.1266034 3.732846 at 60iterations 6.1475493E-02 1.875427 at 70iterations 3.0119162E-02 0.9483643 at 80iterations 1.4771529E-02 0.4407129 at 90iterations 7.2838110E-03 0.2229221 at 100iterations 3.6556416E-03 0.1108475 at 110iterations 1.8880753E-03 6.1008453E-02 at 120iterations finished qdiffx linear iterations at : 12:20:56 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 1.8880753E-03 6.1008453E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 12:20:56 7.899u 0.769s 0:08.95 96.6% 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 Sun Oct 9 2011 at 12:20:56 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 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: 3.032081 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): -14.27500 38.56000 ymin,ymax (A): -0.1560000 44.71900 zmin,zma (A): -7.104000 43.75900 x,y,z range (A): 52.83500 44.87500 50.86300 scale (grids/A): 3.032081 object centre (A): 12.14250 22.28150 18.32750 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500025 assigned positive charge : 373.0132 centred at (gu) : 92.88416 95.00622 89.97234 assigned negative charge : -369.5135 centred at (gu) : 93.73418 95.29935 89.82820 start vw surface at 0.1000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 176449 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21210 grid for indexing accessible points = 1.400000 m= 91330 mr = 126613 m= 35538 mr = 74263 m= 9878 mr = 28707 m= 1768 mr = 7577 m= 148 mr = 1242 m= 4 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 2947 time to turn everything in is 1.110000 number of dielectric boundary points 76634 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 18191 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) : 2.021387 object centre at (A) : 12.14250 22.28150 18.32750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2000234 7.8464992E-02 midg,1,midg; midg,igrid,midg 0.3037701 -9.8098882E-02 1,midg,midg; igrid,midg,midg 0.3520177 -0.4425511 gauss-seidel spectral radius is 0.9992864 estimated iterations to convergence 295 setup time was (sec) 1.350000 now iterating at: 12:20:58 rms-change max change #iterations 10.74588 370.9241 at 10iterations 6.379068 147.7789 at 20iterations 3.785701 70.93792 at 30iterations 2.225792 42.22129 at 40iterations 1.306563 23.26826 at 50iterations 0.7679292 14.40760 at 60iterations 0.4487468 8.415441 at 70iterations 0.2624269 4.568254 at 80iterations 0.1533688 2.928898 at 90iterations 8.9535661E-02 1.593391 at 100iterations 5.2376676E-02 0.8908958 at 110iterations 3.0779226E-02 0.5234318 at 120iterations 1.8072791E-02 0.3228569 at 130iterations 1.0742658E-02 0.2157555 at 140iterations 6.4875991E-03 0.1400261 at 150iterations 4.0404149E-03 8.0911636E-02 at 160iterations 2.6328303E-03 5.7483673E-02 at 170iterations 1.8152734E-03 3.8518906E-02 at 180iterations finished qdiffx linear iterations at : 12:21:10 total time elapsed so far: 13.85000 # loops : 180 mean,max change (kT/e) : 1.8152734E-03 3.8518906E-02 energy calculations done at 13.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.99000 DelPhi exited at 12:21:11 13.990u 0.222s 0:14.54 97.7% 0+0k 0+0io 0pf+0w