Mon Oct 10 14:38:18 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+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 Mon Oct 10 2011 at 14:38:18 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2639 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: 0.6481920 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): -8.235001 45.18800 ymin,ymax (A): -18.46800 29.98200 zmin,zma (A): 17.65000 72.57200 x,y,z range (A): 53.42300 48.45000 54.92200 scale (grids/A): 0.6481920 object centre (A): 18.47650 5.757000 45.11100 number of atom coordinates read : 2639 total number of charged atoms : 2490 net assigned charge : -11.49998 assigned positive charge : 401.4471 centred at (gu) : 88.11131 88.63673 89.76751 assigned negative charge : -412.9475 centred at (gu) : 88.09113 88.42207 89.60738 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7605 nv = 96 ne = 84 npr = 52353 no. pairs analyzed = 52353 no. exposed pairs = 3675 no. arc points = 25760 no. surface atoms = 1214 nbur = 1425 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3921 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3000000 number of dielectric boundary points 4069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2373 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8844 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7613248E-08 3.6375387E-09 midg,1,midg; midg,igrid,midg -7.2297127E-08 8.6684784E-09 1,midg,midg; igrid,midg,midg -3.4646277E-08 -1.1812632E-08 gauss-seidel spectral radius is 0.9876799 estimated iterations to convergence 74 setup time was (sec) 0.5100000 now iterating at: 14:38:18 rms-change max change #iterations 0.1618244 23.74619 at 10iterations 1.6066974E-02 2.393089 at 20iterations 1.6980002E-03 0.2271032 at 30iterations 2.0883362E-04 2.5369644E-02 at 40iterations 3.8136295E-05 3.9768219E-03 at 50iterations finished qdiffx linear iterations at : 14:38:21 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 3.8136295E-05 3.9768219E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 14:38:21 3.106u 0.131s 0:03.58 90.2% 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 Mon Oct 10 2011 at 14:38:21 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2639 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: 1.944576 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): -8.235001 45.18800 ymin,ymax (A): -18.46800 29.98200 zmin,zma (A): 17.65000 72.57200 x,y,z range (A): 53.42300 48.45000 54.92200 scale (grids/A): 1.944576 object centre (A): 18.47650 5.757000 45.11100 number of atom coordinates read : 2639 total number of charged atoms : 2490 net assigned charge : -11.49998 assigned positive charge : 401.4471 centred at (gu) : 84.33338 85.90977 89.30219 assigned negative charge : -412.9475 centred at (gu) : 84.27299 85.26592 88.82174 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81267 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25760 grid for indexing accessible points = 1.400000 m= 29222 mr = 54278 m= 4399 mr = 20728 m= 262 mr = 2509 m= 5 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1872 time to turn everything in is 0.5900000 number of dielectric boundary points 37536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 19597 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) : 0.6481920 object centre at (A) : 18.47650 5.757000 45.11100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8065748E-02 -4.7069597E-03 midg,1,midg; midg,igrid,midg -8.5521296E-02 1.5308271E-02 1,midg,midg; igrid,midg,midg -2.6289692E-02 -2.6517868E-02 gauss-seidel spectral radius is 0.9987077 estimated iterations to convergence 220 setup time was (sec) 0.8800000 now iterating at: 14:38:22 rms-change max change #iterations 4.523995 225.6557 at 10iterations 2.161347 74.06096 at 20iterations 1.030756 32.42738 at 30iterations 0.4925397 15.90852 at 40iterations 0.2345666 7.122824 at 50iterations 0.1122082 3.388565 at 60iterations 5.3667989E-02 1.638769 at 70iterations 2.5642715E-02 0.7973900 at 80iterations 1.2215762E-02 0.4188156 at 90iterations 5.8642426E-03 0.1802158 at 100iterations 2.7891637E-03 8.2843781E-02 at 110iterations 1.3430617E-03 3.8679123E-02 at 120iterations finished qdiffx linear iterations at : 14:38:29 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 1.3430617E-03 3.8679123E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 14:38:30 7.718u 0.208s 0:08.51 92.9% 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 Mon Oct 10 2011 at 14:38:30 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2639 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: 2.916864 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): -8.235001 45.18800 ymin,ymax (A): -18.46800 29.98200 zmin,zma (A): 17.65000 72.57200 x,y,z range (A): 53.42300 48.45000 54.92200 scale (grids/A): 2.916864 object centre (A): 18.47650 5.757000 45.11100 number of atom coordinates read : 2639 total number of charged atoms : 2490 net assigned charge : -11.49998 assigned positive charge : 401.4471 centred at (gu) : 81.50008 83.86469 88.95304 assigned negative charge : -412.9475 centred at (gu) : 81.40951 82.89884 88.23262 start vw surface at 0.1300000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 187643 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25760 grid for indexing accessible points = 1.400000 m= 93917 mr = 131822 m= 33624 mr = 75176 m= 7624 mr = 26118 m= 1067 mr = 5414 m= 65 mr = 690 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 5973 time to turn everything in is 1.430000 number of dielectric boundary points 84695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 19920 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) : 1.944576 object centre at (A) : 18.47650 5.757000 45.11100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5260361 -2.6821027E-02 midg,1,midg; midg,igrid,midg -0.9046934 0.1857990 1,midg,midg; igrid,midg,midg -0.1293544 -0.2084713 gauss-seidel spectral radius is 0.9992921 estimated iterations to convergence 297 setup time was (sec) 1.760000 now iterating at: 14:38:32 rms-change max change #iterations 10.78675 463.2449 at 10iterations 6.404475 172.0351 at 20iterations 3.795237 82.11861 at 30iterations 2.234490 50.78458 at 40iterations 1.313846 25.24364 at 50iterations 0.7715195 14.62735 at 60iterations 0.4518335 8.957640 at 70iterations 0.2652018 5.270063 at 80iterations 0.1550956 3.230011 at 90iterations 9.0677738E-02 2.081599 at 100iterations 5.2941229E-02 1.094175 at 110iterations 3.0901123E-02 0.5807362 at 120iterations 1.8013958E-02 0.3681602 at 130iterations 1.0530712E-02 0.1805406 at 140iterations 6.1317841E-03 0.1237414 at 150iterations 3.5816941E-03 7.0816040E-02 at 160iterations 2.0922786E-03 3.8921356E-02 at 170iterations 1.2219317E-03 2.1230698E-02 at 180iterations finished qdiffx linear iterations at : 14:38:43 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 1.2219317E-03 2.1230698E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.68000 DelPhi exited at 14:38:43 12.685u 0.235s 0:13.37 96.5% 0+0k 0+0io 0pf+0w