Tue Oct 11 05:28:11 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 Tue Oct 11 2011 at 05:28:12 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 = 2035 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: 0.7396942 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): -18.35300 29.77500 ymin,ymax (A): -11.70500 30.73000 zmin,zma (A): -8.557000 38.03500 x,y,z range (A): 48.12800 42.43500 46.59200 scale (grids/A): 0.7396942 object centre (A): 5.711000 9.512500 14.73900 number of atom coordinates read : 2035 total number of charged atoms : 1936 net assigned charge : 6.500009 assigned positive charge : 313.9360 centred at (gu) : 90.32333 89.80212 91.01711 assigned negative charge : -307.4362 centred at (gu) : 90.25574 89.71487 90.90247 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7725 nv = 96 ne = 84 npr = 40102 no. pairs analyzed = 40102 no. exposed pairs = 2497 no. arc points = 17124 no. surface atoms = 852 nbur = 1183 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 611 mr = 4556 m= 4 mr = 127 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 0.2700000 number of dielectric boundary points 3657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1525 ## 135 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8239 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2902673E-09 2.6908060E-07 midg,1,midg; midg,igrid,midg 2.8024749E-08 1.8934905E-07 1,midg,midg; igrid,midg,midg 4.4198394E-08 1.8857411E-07 gauss-seidel spectral radius is 0.9904623 estimated iterations to convergence 83 setup time was (sec) 0.5000000 now iterating at: 05:28:12 rms-change max change #iterations 0.2402372 46.19092 at 10iterations 3.2498825E-02 4.298790 at 20iterations 4.4967029E-03 0.6637173 at 30iterations 6.7857397E-04 8.7430000E-02 at 40iterations 1.3931585E-04 1.7702103E-02 at 50iterations finished qdiffx linear iterations at : 05:28:15 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.3931585E-04 1.7702103E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 05:28:16 3.398u 0.139s 0:04.02 87.5% 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 05:28:16 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 = 2035 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: 2.219083 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): -18.35300 29.77500 ymin,ymax (A): -11.70500 30.73000 zmin,zma (A): -8.557000 38.03500 x,y,z range (A): 48.12800 42.43500 46.59200 scale (grids/A): 2.219083 object centre (A): 5.711000 9.512500 14.73900 number of atom coordinates read : 2035 total number of charged atoms : 1936 net assigned charge : 6.500009 assigned positive charge : 313.9360 centred at (gu) : 90.96994 89.40633 93.05133 assigned negative charge : -307.4362 centred at (gu) : 90.76743 89.14472 92.70752 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80963 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17124 grid for indexing accessible points = 1.400000 m= 34523 mr = 58012 m= 7511 mr = 26731 m= 777 mr = 5193 m= 43 mr = 436 m= 0 mr = 4 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 33441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 15420 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) : 0.7396942 object centre at (A) : 5.711000 9.512500 14.73900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0183345E-02 4.6994265E-02 midg,1,midg; midg,igrid,midg 3.1491250E-02 3.1539373E-02 1,midg,midg; igrid,midg,midg 4.8936341E-02 4.7952157E-02 gauss-seidel spectral radius is 0.9989132 estimated iterations to convergence 240 setup time was (sec) 0.9700000 now iterating at: 05:28:17 rms-change max change #iterations 4.927865 195.0994 at 10iterations 2.497842 83.64928 at 20iterations 1.273032 41.15749 at 30iterations 0.6479688 20.35065 at 40iterations 0.3299217 10.08481 at 50iterations 0.1680302 4.745049 at 60iterations 8.5494272E-02 2.833908 at 70iterations 4.3537583E-02 1.305914 at 80iterations 2.2226270E-02 0.6495841 at 90iterations 1.1361981E-02 0.3350163 at 100iterations 5.8463812E-03 0.1714106 at 110iterations 3.0327763E-03 8.8573456E-02 at 120iterations finished qdiffx linear iterations at : 05:28:24 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 3.0327763E-03 8.8573456E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 05:28:24 7.945u 0.258s 0:08.70 94.1% 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 05:28:24 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 = 2035 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: 3.328624 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): -18.35300 29.77500 ymin,ymax (A): -11.70500 30.73000 zmin,zma (A): -8.557000 38.03500 x,y,z range (A): 48.12800 42.43500 46.59200 scale (grids/A): 3.328624 object centre (A): 5.711000 9.512500 14.73900 number of atom coordinates read : 2035 total number of charged atoms : 1936 net assigned charge : 6.500009 assigned positive charge : 313.9360 centred at (gu) : 91.45492 89.10944 94.57697 assigned negative charge : -307.4362 centred at (gu) : 91.15112 88.71702 94.06129 start vw surface at 0.1400000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 186368 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17124 grid for indexing accessible points = 1.400000 m= 105328 mr = 139307 m= 45928 mr = 88469 m= 14145 mr = 38320 m= 3114 mr = 11237 m= 440 mr = 2324 m= 41 mr = 299 m= 0 mr = 17 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.100000 number of dielectric boundary points 75391 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 15488 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) : 2.219083 object centre at (A) : 5.711000 9.512500 14.73900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5283905 0.4344271 midg,1,midg; midg,igrid,midg 0.2667526 0.1468179 1,midg,midg; igrid,midg,midg 0.3054806 0.2793011 gauss-seidel spectral radius is 0.9993189 estimated iterations to convergence 302 setup time was (sec) 2.440000 now iterating at: 05:28:27 rms-change max change #iterations 10.80256 301.9976 at 10iterations 6.463298 146.9570 at 20iterations 3.851381 68.30243 at 30iterations 2.296785 42.82996 at 40iterations 1.365103 33.71039 at 50iterations 0.8099703 13.65330 at 60iterations 0.4797601 8.089855 at 70iterations 0.2842513 6.838415 at 80iterations 0.1683742 2.772532 at 90iterations 9.9561960E-02 1.665977 at 100iterations 5.9101243E-02 1.148031 at 110iterations 3.4985889E-02 0.6372433 at 120iterations 2.0923482E-02 0.3488288 at 130iterations 1.2629705E-02 0.2098303 at 140iterations 7.7869636E-03 0.1441154 at 150iterations 4.9687251E-03 8.6779594E-02 at 160iterations 3.3200684E-03 6.4243317E-02 at 170iterations 2.3656175E-03 3.9508820E-02 at 180iterations finished qdiffx linear iterations at : 05:28:38 total time elapsed so far: 13.72000 # loops : 180 mean,max change (kT/e) : 2.3656175E-03 3.9508820E-02 energy calculations done at 13.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.92000 DelPhi exited at 05:28:39 13.919u 0.262s 0:14.65 96.7% 0+0k 0+0io 0pf+0w