Sat Oct 15 15:29:29 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 15 2011 at 15:29:29 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2822 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6454771 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): -12.21500 36.39800 ymin,ymax (A): -25.61200 22.07700 zmin,zma (A): -10.21600 44.93700 x,y,z range (A): 48.61300 47.68900 55.15300 scale (grids/A): 0.6454771 object centre (A): 12.09150 -1.767500 17.36050 number of atom coordinates read : 2822 total number of charged atoms : 2668 net assigned charge : 0.1620203 assigned positive charge : 428.7037 centred at (gu) : 90.15523 90.65564 91.95867 assigned negative charge : -428.5422 centred at (gu) : 89.87209 90.55920 91.88664 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7510 nv = 96 ne = 84 npr = 59695 no. pairs analyzed = 59695 no. exposed pairs = 3272 no. arc points = 22733 no. surface atoms = 1104 nbur = 1718 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 417 mr = 4254 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2280 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9298 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.1351969E-09 1.6228256E-08 midg,1,midg; midg,igrid,midg -1.2635410E-08 1.6297738E-08 1,midg,midg; igrid,midg,midg -4.2058758E-08 4.2183547E-08 gauss-seidel spectral radius is 0.9875728 estimated iterations to convergence 73 setup time was (sec) 0.4700000 now iterating at: 15:29:29 rms-change max change #iterations 0.1608746 27.17968 at 10iterations 1.6568253E-02 2.234335 at 20iterations 1.7834583E-03 0.2355080 at 30iterations 2.1822799E-04 3.3526421E-02 at 40iterations 3.9188224E-05 5.1364899E-03 at 50iterations finished qdiffx linear iterations at : 15:29:33 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 3.9188224E-05 5.1364899E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 15:29:33 4.026u 0.252s 0:04.57 93.4% 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 Sat Oct 15 2011 at 15:29:33 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2822 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.936431 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): -12.21500 36.39800 ymin,ymax (A): -25.61200 22.07700 zmin,zma (A): -10.21600 44.93700 x,y,z range (A): 48.61300 47.68900 55.15300 scale (grids/A): 1.936431 object centre (A): 12.09150 -1.767500 17.36050 number of atom coordinates read : 2822 total number of charged atoms : 2668 net assigned charge : 0.1620203 assigned positive charge : 428.7037 centred at (gu) : 90.46536 91.96658 95.87542 assigned negative charge : -428.5422 centred at (gu) : 89.61599 91.67695 95.65967 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81818 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22733 grid for indexing accessible points = 1.400000 m= 29173 mr = 58143 m= 4529 mr = 21530 m= 293 mr = 2766 m= 9 mr = 118 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 3236 time to turn everything in is 0.4200000 number of dielectric boundary points 33263 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 21012 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) : 0.6454771 object centre at (A) : 12.09150 -1.767500 17.36050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3237986E-02 6.1124214E-03 midg,1,midg; midg,igrid,midg -1.5173567E-02 1.8804277E-03 1,midg,midg; igrid,midg,midg -2.0416033E-02 6.1203338E-02 gauss-seidel spectral radius is 0.9986903 estimated iterations to convergence 219 setup time was (sec) 0.6900000 now iterating at: 15:29:34 rms-change max change #iterations 4.635066 209.4840 at 10iterations 2.207948 68.93143 at 20iterations 1.052624 30.51825 at 30iterations 0.5020248 15.59202 at 40iterations 0.2390057 7.654139 at 50iterations 0.1138615 3.306519 at 60iterations 5.4344546E-02 1.606265 at 70iterations 2.5924861E-02 0.8855982 at 80iterations 1.2331880E-02 0.3863064 at 90iterations 5.8609461E-03 0.2056603 at 100iterations 2.8032945E-03 8.2420349E-02 at 110iterations 1.3342933E-03 4.3462753E-02 at 120iterations finished qdiffx linear iterations at : 15:29:43 total time elapsed so far: 9.310000 # loops : 120 mean,max change (kT/e) : 1.3342933E-03 4.3462753E-02 energy calculations done at 9.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.450000 DelPhi exited at 15:29:43 9.456u 0.316s 0:10.16 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 Sat Oct 15 2011 at 15:29:44 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2822 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.904647 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): -12.21500 36.39800 ymin,ymax (A): -25.61200 22.07700 zmin,zma (A): -10.21600 44.93700 x,y,z range (A): 48.61300 47.68900 55.15300 scale (grids/A): 2.904647 object centre (A): 12.09150 -1.767500 17.36050 number of atom coordinates read : 2822 total number of charged atoms : 2668 net assigned charge : 0.1620203 assigned positive charge : 428.7037 centred at (gu) : 90.69778 92.94972 98.81286 assigned negative charge : -428.5422 centred at (gu) : 89.42387 92.51535 98.48923 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 189293 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22733 grid for indexing accessible points = 1.400000 m= 95276 mr = 140584 m= 33784 mr = 78397 m= 8055 mr = 27016 m= 1159 mr = 5942 m= 98 mr = 722 m= 4 mr = 44 m= 0 mr = 3 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 10481 time to turn everything in is 1.140000 number of dielectric boundary points 74961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 21331 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) : 1.936431 object centre at (A) : 12.09150 -1.767500 17.36050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5535102 0.3250954 midg,1,midg; midg,igrid,midg -0.1780436 4.6502594E-02 1,midg,midg; igrid,midg,midg -0.1646086 0.5238490 gauss-seidel spectral radius is 0.9992689 estimated iterations to convergence 292 setup time was (sec) 1.460000 now iterating at: 15:29:45 rms-change max change #iterations 10.77987 372.4195 at 10iterations 6.307817 125.3734 at 20iterations 3.676883 71.03806 at 30iterations 2.135956 39.34564 at 40iterations 1.241457 22.61229 at 50iterations 0.7195322 13.30038 at 60iterations 0.4170868 7.024956 at 70iterations 0.2413241 4.148894 at 80iterations 0.1395119 2.455450 at 90iterations 8.0679506E-02 1.442368 at 100iterations 4.6659090E-02 0.8999424 at 110iterations 2.7072530E-02 0.5009054 at 120iterations 1.5644128E-02 0.2688255 at 130iterations 9.0801818E-03 0.1565266 at 140iterations 5.2879401E-03 9.7356796E-02 at 150iterations 3.0907721E-03 5.1059246E-02 at 160iterations 1.8291232E-03 3.1064987E-02 at 170iterations 1.0997086E-03 1.8180847E-02 at 180iterations finished qdiffx linear iterations at : 15:29:59 total time elapsed so far: 15.55000 # loops : 180 mean,max change (kT/e) : 1.0997086E-03 1.8180847E-02 energy calculations done at 15.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.69000 DelPhi exited at 15:30:00 15.689u 0.307s 0:16.29 98.0% 0+0k 0+0io 0pf+0w