Sat Oct 8 21:46:06 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+sph.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 = amb.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 8 2011 at 21:46:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2038 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6646379 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): 6.341000 59.90400 ymin,ymax (A): 2.891000 50.08300 zmin,zma (A): 13.35500 56.01900 x,y,z range (A): 53.56300 47.19200 42.66400 scale (grids/A): 0.6646379 object centre (A): 33.12250 26.48700 34.68700 number of atom coordinates read : 2038 total number of charged atoms : 1902 net assigned charge : 1.000003 assigned positive charge : 302.8528 centred at (gu) : 87.71337 89.31104 89.36885 assigned negative charge : -301.8529 centred at (gu) : 87.85599 89.38508 89.41486 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6082 nv = 96 ne = 84 npr = 41089 no. pairs analyzed = 41089 no. exposed pairs = 2574 no. arc points = 18445 no. surface atoms = 863 nbur = 1175 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 379 mr = 3340 m= 1 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.1600000 number of dielectric boundary points 3065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1710 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6996 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1389709E-08 -5.1111706E-09 midg,1,midg; midg,igrid,midg 1.7042945E-08 -9.2766381E-09 1,midg,midg; igrid,midg,midg 4.2760803E-08 -1.4129843E-08 gauss-seidel spectral radius is 0.9882160 estimated iterations to convergence 75 setup time was (sec) 0.3400000 now iterating at: 21:46:06 rms-change max change #iterations 0.1488493 22.44106 at 10iterations 1.6051579E-02 2.584966 at 20iterations 1.7429967E-03 0.2704620 at 30iterations 1.8583701E-04 2.6241302E-02 at 40iterations 2.1228239E-05 3.0641556E-03 at 50iterations finished qdiffx linear iterations at : 21:46:09 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 2.1228239E-05 3.0641556E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 21:46:10 3.327u 0.168s 0:03.77 92.3% 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 8 2011 at 21:46:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2038 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.993914 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): 6.341000 59.90400 ymin,ymax (A): 2.891000 50.08300 zmin,zma (A): 13.35500 56.01900 x,y,z range (A): 53.56300 47.19200 42.66400 scale (grids/A): 1.993914 object centre (A): 33.12250 26.48700 34.68700 number of atom coordinates read : 2038 total number of charged atoms : 1902 net assigned charge : 1.000003 assigned positive charge : 302.8528 centred at (gu) : 83.14002 87.93272 88.10647 assigned negative charge : -301.8529 centred at (gu) : 83.56793 88.15514 88.24434 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 65073 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18445 grid for indexing accessible points = 1.400000 m= 23914 mr = 44622 m= 4438 mr = 17538 m= 337 mr = 2973 m= 5 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1733 time to turn everything in is 0.3200000 number of dielectric boundary points 28495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 15018 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) : 0.6646379 object centre at (A) : 33.12250 26.48700 34.68700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1641191E-02 -5.4118433E-04 midg,1,midg; midg,igrid,midg 3.4340464E-02 1.8817201E-03 1,midg,midg; igrid,midg,midg -3.3821467E-02 -4.3239072E-02 gauss-seidel spectral radius is 0.9986932 estimated iterations to convergence 219 setup time was (sec) 0.5300000 now iterating at: 21:46:10 rms-change max change #iterations 4.072241 194.1471 at 10iterations 1.930075 70.18551 at 20iterations 0.9185205 31.82465 at 30iterations 0.4386388 16.72715 at 40iterations 0.2088614 6.922475 at 50iterations 9.9324420E-02 3.126039 at 60iterations 4.7259737E-02 1.607283 at 70iterations 2.2500282E-02 0.7258224 at 80iterations 1.0688284E-02 0.3655701 at 90iterations 5.0923806E-03 0.1716080 at 100iterations 2.4322877E-03 7.8086853E-02 at 110iterations 1.1603493E-03 3.9458275E-02 at 120iterations finished qdiffx linear iterations at : 21:46:17 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 1.1603493E-03 3.9458275E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 21:46:18 7.633u 0.211s 0:08.14 96.3% 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 8 2011 at 21:46:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2038 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.990870 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): 6.341000 59.90400 ymin,ymax (A): 2.891000 50.08300 zmin,zma (A): 13.35500 56.01900 x,y,z range (A): 53.56300 47.19200 42.66400 scale (grids/A): 2.990870 object centre (A): 33.12250 26.48700 34.68700 number of atom coordinates read : 2038 total number of charged atoms : 1902 net assigned charge : 1.000003 assigned positive charge : 302.8528 centred at (gu) : 79.70994 86.89910 87.15974 assigned negative charge : -301.8529 centred at (gu) : 80.35190 87.23261 87.36649 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 150391 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18445 grid for indexing accessible points = 1.400000 m= 75780 mr = 108204 m= 29071 mr = 61669 m= 8257 mr = 23445 m= 1508 mr = 6411 m= 85 mr = 1115 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 6086 time to turn everything in is 0.8500000 number of dielectric boundary points 64201 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 15216 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) : 1.993914 object centre at (A) : 33.12250 26.48700 34.68700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1390017 -1.0244998E-02 midg,1,midg; midg,igrid,midg 0.3008188 -6.0033247E-02 1,midg,midg; igrid,midg,midg -0.5694275 -0.5397874 gauss-seidel spectral radius is 0.9992645 estimated iterations to convergence 291 setup time was (sec) 1.080000 now iterating at: 21:46:19 rms-change max change #iterations 9.404970 394.8062 at 10iterations 5.523006 134.4872 at 20iterations 3.220686 69.64957 at 30iterations 1.873240 39.96476 at 40iterations 1.088821 23.63146 at 50iterations 0.6305979 12.52813 at 60iterations 0.3649287 7.811424 at 70iterations 0.2113182 3.895365 at 80iterations 0.1220776 2.683651 at 90iterations 7.0350125E-02 1.311867 at 100iterations 4.0565763E-02 0.7658997 at 110iterations 2.3340065E-02 0.4905167 at 120iterations 1.3457632E-02 0.2542229 at 130iterations 7.7635669E-03 0.1409016 at 140iterations 4.4770553E-03 8.7684631E-02 at 150iterations 2.5779018E-03 4.8484802E-02 at 160iterations 1.4836126E-03 2.8220415E-02 at 170iterations 8.5280521E-04 1.6584873E-02 at 180iterations finished qdiffx linear iterations at : 21:46:30 total time elapsed so far: 12.21000 # loops : 180 mean,max change (kT/e) : 8.5280521E-04 1.6584873E-02 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 21:46:31 12.339u 0.208s 0:12.81 97.8% 0+0k 0+0io 0pf+0w