Tue Oct 11 08:30:17 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 Tue Oct 11 2011 at 08:30:17 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6182165 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): -13.36700 44.21800 ymin,ymax (A): -9.081000 43.95500 zmin,zma (A): -25.52000 29.98600 x,y,z range (A): 57.58500 53.03600 55.50600 scale (grids/A): 0.6182165 object centre (A): 15.42550 17.43700 2.233000 number of atom coordinates read : 3033 total number of charged atoms : 2863 net assigned charge : -3.908984 assigned positive charge : 465.0033 centred at (gu) : 91.37466 90.27426 90.46303 assigned negative charge : -468.9129 centred at (gu) : 91.18744 90.12959 90.49451 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7276 nv = 96 ne = 84 npr = 63244 no. pairs analyzed = 63244 no. exposed pairs = 3589 no. arc points = 24403 no. surface atoms = 1206 nbur = 1827 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 306 mr = 4080 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2411 ## 249 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9260 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.3793427E-10 -6.1959682E-09 midg,1,midg; midg,igrid,midg -1.3538294E-08 8.1465545E-09 1,midg,midg; igrid,midg,midg -1.3093032E-08 1.4777131E-08 gauss-seidel spectral radius is 0.9864764 estimated iterations to convergence 70 setup time was (sec) 0.5400000 now iterating at: 08:30:18 rms-change max change #iterations 0.1396768 19.51244 at 10iterations 1.2885364E-02 1.906003 at 20iterations 1.3343096E-03 0.1832047 at 30iterations 1.8425475E-04 2.3946762E-02 at 40iterations 4.0474701E-05 4.8017502E-03 at 50iterations finished qdiffx linear iterations at : 08:30:21 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 4.0474701E-05 4.8017502E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 08:30:21 3.133u 0.129s 0:03.70 87.8% 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 Tue Oct 11 2011 at 08:30:21 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.854650 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): -13.36700 44.21800 ymin,ymax (A): -9.081000 43.95500 zmin,zma (A): -25.52000 29.98600 x,y,z range (A): 57.58500 53.03600 55.50600 scale (grids/A): 1.854650 object centre (A): 15.42550 17.43700 2.233000 number of atom coordinates read : 3033 total number of charged atoms : 2863 net assigned charge : -3.908984 assigned positive charge : 465.0033 centred at (gu) : 94.12351 90.82220 91.38824 assigned negative charge : -468.9129 centred at (gu) : 93.56178 90.38826 91.48331 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24403 grid for indexing accessible points = 1.400000 m= 26757 mr = 56642 m= 3483 mr = 19404 m= 184 mr = 2063 m= 4 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1539 time to turn everything in is 0.5600000 number of dielectric boundary points 32350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 22415 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) : 0.6182165 object centre at (A) : 15.42550 17.43700 2.233000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5660018E-02 -1.3013461E-02 midg,1,midg; midg,igrid,midg -3.2839533E-02 -1.7012813E-03 1,midg,midg; igrid,midg,midg -9.2322510E-03 4.1466687E-02 gauss-seidel spectral radius is 0.9985933 estimated iterations to convergence 211 setup time was (sec) 0.8100000 now iterating at: 08:30:22 rms-change max change #iterations 4.510945 207.3606 at 10iterations 2.090678 68.78018 at 20iterations 0.9715982 34.16513 at 30iterations 0.4507511 14.02669 at 40iterations 0.2089788 6.446812 at 50iterations 9.6950948E-02 3.048491 at 60iterations 4.4996534E-02 1.437319 at 70iterations 2.0889649E-02 0.5978165 at 80iterations 9.7213322E-03 0.2938538 at 90iterations 4.5371931E-03 0.1295776 at 100iterations 2.1197444E-03 6.7936897E-02 at 110iterations 9.9682750E-04 3.1442642E-02 at 120iterations finished qdiffx linear iterations at : 08:30:28 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 9.9682750E-04 3.1442642E-02 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.120000 DelPhi exited at 08:30:29 7.122u 0.157s 0:07.59 95.7% 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 Tue Oct 11 2011 at 08:30:29 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.781974 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): -13.36700 44.21800 ymin,ymax (A): -9.081000 43.95500 zmin,zma (A): -25.52000 29.98600 x,y,z range (A): 57.58500 53.03600 55.50600 scale (grids/A): 2.781974 object centre (A): 15.42550 17.43700 2.233000 number of atom coordinates read : 3033 total number of charged atoms : 2863 net assigned charge : -3.908984 assigned positive charge : 465.0033 centred at (gu) : 96.18497 91.23323 92.08229 assigned negative charge : -468.9129 centred at (gu) : 95.34261 90.58245 92.22485 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 185748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24403 grid for indexing accessible points = 1.400000 m= 89878 mr = 137620 m= 28894 mr = 73091 m= 6044 mr = 22842 m= 794 mr = 4359 m= 47 mr = 476 m= 3 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.7600001 no. cavity mid-points inaccessible to solvent = 5151 time to turn everything in is 1.360000 number of dielectric boundary points 73008 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 22900 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) : 1.854650 object centre at (A) : 15.42550 17.43700 2.233000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4904560 1.3265755E-02 midg,1,midg; midg,igrid,midg -0.4229776 -6.2507883E-02 1,midg,midg; igrid,midg,midg -6.3028686E-02 0.5671396 gauss-seidel spectral radius is 0.9992499 estimated iterations to convergence 288 setup time was (sec) 1.640000 now iterating at: 08:30:31 rms-change max change #iterations 10.55750 330.7576 at 10iterations 6.148590 154.1308 at 20iterations 3.555048 65.00021 at 30iterations 2.051549 43.29867 at 40iterations 1.184094 23.82056 at 50iterations 0.6805255 12.66482 at 60iterations 0.3906575 6.889401 at 70iterations 0.2245784 4.225231 at 80iterations 0.1289963 2.328666 at 90iterations 7.4004322E-02 1.285533 at 100iterations 4.2413194E-02 0.7492867 at 110iterations 2.4453592E-02 0.4417295 at 120iterations 1.4046920E-02 0.2555313 at 130iterations 8.1042610E-03 0.1485863 at 140iterations 4.6982709E-03 7.8502655E-02 at 150iterations 2.7406972E-03 4.8255920E-02 at 160iterations 1.6206456E-03 3.0178070E-02 at 170iterations 9.7487937E-04 1.8104553E-02 at 180iterations finished qdiffx linear iterations at : 08:30:40 total time elapsed so far: 11.00000 # loops : 180 mean,max change (kT/e) : 9.7487937E-04 1.8104553E-02 energy calculations done at 11.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.17000 DelPhi exited at 08:30:41 11.174u 0.166s 0:11.72 96.6% 0+0k 0+0io 0pf+0w