Sat Oct 15 15:55:24 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 15 2011 at 15:55:24 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 = 2080 !!! WARNING: ASN 245 has a net charge of -0.5000 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: 0.7304662 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): -13.83800 34.89800 ymin,ymax (A): -22.14500 25.03400 zmin,zma (A): -13.57400 28.69200 x,y,z range (A): 48.73600 47.17900 42.26600 scale (grids/A): 0.7304662 object centre (A): 10.53000 1.444500 7.559000 number of atom coordinates read : 2080 total number of charged atoms : 1952 net assigned charge : 7.000009 assigned positive charge : 316.5540 centred at (gu) : 88.93791 88.94333 90.13396 assigned negative charge : -309.5542 centred at (gu) : 89.02837 89.05757 90.20261 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7580 nv = 96 ne = 84 npr = 41715 no. pairs analyzed = 41715 no. exposed pairs = 2516 no. arc points = 17504 no. surface atoms = 848 nbur = 1232 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 521 mr = 4416 m= 3 mr = 84 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 3604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1580 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8160 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4931993E-07 4.3405578E-08 midg,1,midg; midg,igrid,midg 2.3101593E-07 5.1628168E-09 1,midg,midg; igrid,midg,midg 2.0814444E-07 2.1082315E-08 gauss-seidel spectral radius is 0.9902256 estimated iterations to convergence 82 setup time was (sec) 0.5200000 now iterating at: 15:55:24 rms-change max change #iterations 0.2287991 30.18050 at 10iterations 3.0293804E-02 4.116905 at 20iterations 4.0921532E-03 0.5305901 at 30iterations 6.1759824E-04 7.1754456E-02 at 40iterations 1.2647024E-04 1.7288208E-02 at 50iterations finished qdiffx linear iterations at : 15:55:27 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.2647024E-04 1.7288208E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 15:55:28 3.415u 0.158s 0:03.96 89.8% 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 Sat Oct 15 2011 at 15:55:28 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 = 2080 !!! WARNING: ASN 245 has a net charge of -0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.191399 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): -13.83800 34.89800 ymin,ymax (A): -22.14500 25.03400 zmin,zma (A): -13.57400 28.69200 x,y,z range (A): 48.73600 47.17900 42.26600 scale (grids/A): 2.191399 object centre (A): 10.53000 1.444500 7.559000 number of atom coordinates read : 2080 total number of charged atoms : 1952 net assigned charge : 7.000009 assigned positive charge : 316.5540 centred at (gu) : 86.81380 86.82997 90.40180 assigned negative charge : -309.5542 centred at (gu) : 87.08507 87.17297 90.60786 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80283 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17504 grid for indexing accessible points = 1.400000 m= 33118 mr = 57312 m= 6598 mr = 25436 m= 624 mr = 4464 m= 22 mr = 311 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 33122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15534 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) : 0.7304662 object centre at (A) : 10.53000 1.444500 7.559000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6236549E-02 2.8006837E-02 midg,1,midg; midg,igrid,midg 5.2108638E-02 -4.1850325E-02 1,midg,midg; igrid,midg,midg 0.1018949 5.3028639E-02 gauss-seidel spectral radius is 0.9988938 estimated iterations to convergence 238 setup time was (sec) 0.9100000 now iterating at: 15:55:29 rms-change max change #iterations 4.854171 227.4417 at 10iterations 2.448103 77.73224 at 20iterations 1.240639 38.46706 at 30iterations 0.6262879 18.19651 at 40iterations 0.3175882 9.255836 at 50iterations 0.1608895 4.629175 at 60iterations 8.1272319E-02 2.267592 at 70iterations 4.1228108E-02 1.224409 at 80iterations 2.0847823E-02 0.5758374 at 90iterations 1.0635155E-02 0.3428802 at 100iterations 5.4444373E-03 0.1774054 at 110iterations 2.8011568E-03 7.9948425E-02 at 120iterations finished qdiffx linear iterations at : 15:55:35 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 2.8011568E-03 7.9948425E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 15:55:36 7.821u 0.177s 0:08.32 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 15:55:36 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 = 2080 !!! WARNING: ASN 245 has a net charge of -0.5000 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: 3.287098 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): -13.83800 34.89800 ymin,ymax (A): -22.14500 25.03400 zmin,zma (A): -13.57400 28.69200 x,y,z range (A): 48.73600 47.17900 42.26600 scale (grids/A): 3.287098 object centre (A): 10.53000 1.444500 7.559000 number of atom coordinates read : 2080 total number of charged atoms : 1952 net assigned charge : 7.000009 assigned positive charge : 316.5540 centred at (gu) : 85.22066 85.24487 90.60278 assigned negative charge : -309.5542 centred at (gu) : 85.62766 85.75935 90.91180 start vw surface at 0.1400000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 184980 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17504 grid for indexing accessible points = 1.400000 m= 102314 mr = 137823 m= 42440 mr = 85796 m= 12566 mr = 35174 m= 2544 mr = 9782 m= 352 mr = 1824 m= 20 mr = 234 m= 0 mr = 7 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.010000 number of dielectric boundary points 74576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 15616 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) : 2.191399 object centre at (A) : 10.53000 1.444500 7.559000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1307179 0.2556029 midg,1,midg; midg,igrid,midg 0.4606570 -0.4968362 1,midg,midg; igrid,midg,midg 0.8086356 0.3371854 gauss-seidel spectral radius is 0.9993139 estimated iterations to convergence 301 setup time was (sec) 2.320000 now iterating at: 15:55:39 rms-change max change #iterations 10.63197 301.0049 at 10iterations 6.309319 191.3842 at 20iterations 3.745259 67.60912 at 30iterations 2.222774 48.78493 at 40iterations 1.315667 22.46583 at 50iterations 0.7773347 19.53600 at 60iterations 0.4591021 8.322367 at 70iterations 0.2708689 4.639091 at 80iterations 0.1596989 2.576466 at 90iterations 9.4203278E-02 1.761198 at 100iterations 5.5829480E-02 0.8934174 at 110iterations 3.3031560E-02 0.5608139 at 120iterations 1.9593939E-02 0.3470459 at 130iterations 1.1784699E-02 0.2100105 at 140iterations 7.1946140E-03 0.1273069 at 150iterations 4.5205932E-03 7.4456215E-02 at 160iterations 2.9524127E-03 5.2136898E-02 at 170iterations 2.0436198E-03 3.3767700E-02 at 180iterations finished qdiffx linear iterations at : 15:55:49 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 2.0436198E-03 3.3767700E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 15:55:50 13.233u 0.175s 0:13.70 97.8% 0+0k 0+0io 0pf+0w