Tue Oct 11 05:27:18 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 05:27:18 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2007 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: MG8 872 has a net charge of 1.4000 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: 0.7174816 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): 25.75000 72.52300 ymin,ymax (A): -20.50600 29.11200 zmin,zma (A): 3.922000 46.51600 x,y,z range (A): 46.77300 49.61800 42.59400 scale (grids/A): 0.7174816 object centre (A): 49.13650 4.302999 25.21900 number of atom coordinates read : 2007 total number of charged atoms : 1924 net assigned charge : 8.331010 assigned positive charge : 312.6071 centred at (gu) : 89.06372 91.17655 90.14740 assigned negative charge : -304.2762 centred at (gu) : 89.19839 91.05872 90.20200 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7190 nv = 96 ne = 84 npr = 39065 no. pairs analyzed = 39065 no. exposed pairs = 2489 no. arc points = 17190 no. surface atoms = 851 nbur = 1156 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 499 mr = 4113 m= 5 mr = 101 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 0.2900000 number of dielectric boundary points 3480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1620 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7887 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1637902E-07 5.5507829E-08 midg,1,midg; midg,igrid,midg 1.3255155E-08 1.9676104E-07 1,midg,midg; igrid,midg,midg 1.9971921E-07 5.0530993E-09 gauss-seidel spectral radius is 0.9898667 estimated iterations to convergence 81 setup time was (sec) 0.5200000 now iterating at: 05:27:19 rms-change max change #iterations 0.2112553 29.08502 at 10iterations 2.6911339E-02 3.856475 at 20iterations 3.7079016E-03 0.4970016 at 30iterations 6.0283317E-04 7.3411942E-02 at 40iterations 1.3958866E-04 1.6052246E-02 at 50iterations finished qdiffx linear iterations at : 05:27:21 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 1.3958866E-04 1.6052246E-02 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 05:27:22 3.353u 0.144s 0:04.04 86.3% 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 Tue Oct 11 2011 at 05:27:22 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2007 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: MG8 872 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.152445 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): 25.75000 72.52300 ymin,ymax (A): -20.50600 29.11200 zmin,zma (A): 3.922000 46.51600 x,y,z range (A): 46.77300 49.61800 42.59400 scale (grids/A): 2.152445 object centre (A): 49.13650 4.302999 25.21900 number of atom coordinates read : 2007 total number of charged atoms : 1924 net assigned charge : 8.331010 assigned positive charge : 312.6071 centred at (gu) : 87.19127 93.52979 90.44237 assigned negative charge : -304.2762 centred at (gu) : 87.59526 93.17628 90.60596 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75534 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17190 grid for indexing accessible points = 1.400000 m= 31559 mr = 53427 m= 6499 mr = 24189 m= 586 mr = 4385 m= 19 mr = 275 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 31919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15292 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) : 0.7174816 object centre at (A) : 49.13650 4.302999 25.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9171988E-02 3.4236062E-02 midg,1,midg; midg,igrid,midg 3.2855831E-02 0.1121975 1,midg,midg; igrid,midg,midg 5.2027378E-02 -3.5683200E-02 gauss-seidel spectral radius is 0.9988564 estimated iterations to convergence 234 setup time was (sec) 0.8900000 now iterating at: 05:27:23 rms-change max change #iterations 4.692757 191.8209 at 10iterations 2.338269 74.38524 at 20iterations 1.169570 37.84823 at 30iterations 0.5864737 19.27977 at 40iterations 0.2937239 9.481709 at 50iterations 0.1463712 4.490745 at 60iterations 7.3180541E-02 2.517061 at 70iterations 3.6838446E-02 1.137701 at 80iterations 1.8562334E-02 0.5712700 at 90iterations 9.3308622E-03 0.3145714 at 100iterations 4.7436277E-03 0.1431808 at 110iterations 2.4616173E-03 7.0346832E-02 at 120iterations finished qdiffx linear iterations at : 05:27:30 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 2.4616173E-03 7.0346832E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 05:27:30 7.553u 0.171s 0:08.18 94.3% 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 Tue Oct 11 2011 at 05:27:30 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2007 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: MG8 872 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.228667 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): 25.75000 72.52300 ymin,ymax (A): -20.50600 29.11200 zmin,zma (A): 3.922000 46.51600 x,y,z range (A): 46.77300 49.61800 42.59400 scale (grids/A): 3.228667 object centre (A): 49.13650 4.302999 25.21900 number of atom coordinates read : 2007 total number of charged atoms : 1924 net assigned charge : 8.331010 assigned positive charge : 312.6071 centred at (gu) : 85.78691 95.29470 90.66365 assigned negative charge : -304.2762 centred at (gu) : 86.39286 94.76446 90.90897 start vw surface at 0.1400000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 173876 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17190 grid for indexing accessible points = 1.400000 m= 96853 mr = 128551 m= 41204 mr = 80755 m= 12205 mr = 34092 m= 2451 mr = 9601 m= 261 mr = 1746 m= 16 mr = 166 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.900000 number of dielectric boundary points 71948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 15392 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) : 2.152445 object centre at (A) : 49.13650 4.302999 25.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1685586 0.2819578 midg,1,midg; midg,igrid,midg 0.2143352 1.042783 1,midg,midg; igrid,midg,midg 0.4625192 -0.4040892 gauss-seidel spectral radius is 0.9993078 estimated iterations to convergence 300 setup time was (sec) 2.190000 now iterating at: 05:27:33 rms-change max change #iterations 10.49446 356.0805 at 10iterations 6.244701 143.5012 at 20iterations 3.714956 72.23851 at 30iterations 2.207489 45.44910 at 40iterations 1.309144 24.70506 at 50iterations 0.7739781 14.87436 at 60iterations 0.4566224 8.287712 at 70iterations 0.2698279 5.589434 at 80iterations 0.1590320 3.006496 at 90iterations 9.4036140E-02 1.788200 at 100iterations 5.5450503E-02 1.069462 at 110iterations 3.2911915E-02 0.5809326 at 120iterations 1.9739119E-02 0.3778152 at 130iterations 1.2031023E-02 0.2252560 at 140iterations 7.5185951E-03 0.1488476 at 150iterations 4.9096309E-03 9.3280792E-02 at 160iterations 3.3992191E-03 6.3701630E-02 at 170iterations 2.4902271E-03 4.4868469E-02 at 180iterations finished qdiffx linear iterations at : 05:27:44 total time elapsed so far: 13.19000 # loops : 180 mean,max change (kT/e) : 2.4902271E-03 4.4868469E-02 energy calculations done at 13.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.40000 DelPhi exited at 05:27:45 13.405u 0.197s 0:14.25 95.3% 0+0k 0+0io 0pf+0w