Tue Oct 11 04:48:16 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 04:48:16 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 !!! 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: 0.6541712 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): -12.27800 37.20400 ymin,ymax (A): -26.02100 22.58600 zmin,zma (A): -8.918000 45.50200 x,y,z range (A): 49.48200 48.60700 54.42000 scale (grids/A): 0.6541712 object centre (A): 12.46300 -1.717500 18.29200 number of atom coordinates read : 2754 total number of charged atoms : 2602 net assigned charge : 3.140012 assigned positive charge : 414.7487 centred at (gu) : 90.28262 90.60385 91.56304 assigned negative charge : -411.6093 centred at (gu) : 90.02671 90.41026 91.50669 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7946 nv = 96 ne = 84 npr = 56196 no. pairs analyzed = 56196 no. exposed pairs = 3287 no. arc points = 22934 no. surface atoms = 1117 nbur = 1637 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 428 mr = 4583 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.3100000 number of dielectric boundary points 3741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2250 ## 230 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9397 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6912903E-09 2.2845771E-08 midg,1,midg; midg,igrid,midg -2.5678426E-08 4.6035783E-08 1,midg,midg; igrid,midg,midg -3.8607954E-08 5.4352864E-08 gauss-seidel spectral radius is 0.9878999 estimated iterations to convergence 74 setup time was (sec) 0.5300000 now iterating at: 04:48:17 rms-change max change #iterations 0.1637660 22.54308 at 10iterations 1.7509501E-02 2.692039 at 20iterations 1.8228829E-03 0.2642937 at 30iterations 1.9641028E-04 2.6762009E-02 at 40iterations 2.3467490E-05 3.8948059E-03 at 50iterations finished qdiffx linear iterations at : 04:48:19 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 2.3467490E-05 3.8948059E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 04:48:20 3.105u 0.133s 0:03.69 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 04:48:20 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 !!! 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: 1.962514 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): -12.27800 37.20400 ymin,ymax (A): -26.02100 22.58600 zmin,zma (A): -8.918000 45.50200 x,y,z range (A): 49.48200 48.60700 54.42000 scale (grids/A): 1.962514 object centre (A): 12.46300 -1.717500 18.29200 number of atom coordinates read : 2754 total number of charged atoms : 2602 net assigned charge : 3.140012 assigned positive charge : 414.7487 centred at (gu) : 90.84738 91.81109 94.68834 assigned negative charge : -411.6093 centred at (gu) : 90.07973 91.23058 94.51994 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84857 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22934 grid for indexing accessible points = 1.400000 m= 32235 mr = 60325 m= 5355 mr = 24475 m= 305 mr = 3459 m= 7 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1222 time to turn everything in is 0.5900000 number of dielectric boundary points 34376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 20533 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) : 0.6541712 object centre at (A) : 12.46300 -1.717500 18.29200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8274238E-02 1.2857933E-02 midg,1,midg; midg,igrid,midg -1.2194650E-02 3.4797281E-02 1,midg,midg; igrid,midg,midg -1.2968763E-02 5.9355721E-02 gauss-seidel spectral radius is 0.9987244 estimated iterations to convergence 222 setup time was (sec) 0.8500000 now iterating at: 04:48:21 rms-change max change #iterations 4.672781 197.6252 at 10iterations 2.250844 69.53249 at 20iterations 1.083669 31.83468 at 30iterations 0.5223918 15.52480 at 40iterations 0.2515321 8.453238 at 50iterations 0.1214392 3.632587 at 60iterations 5.8130432E-02 1.631166 at 70iterations 2.8112439E-02 0.8161001 at 80iterations 1.3487102E-02 0.3846579 at 90iterations 6.4963824E-03 0.1959743 at 100iterations 3.1273765E-03 8.7583542E-02 at 110iterations 1.5047182E-03 4.3010712E-02 at 120iterations finished qdiffx linear iterations at : 04:48:27 total time elapsed so far: 7.140000 # loops : 120 mean,max change (kT/e) : 1.5047182E-03 4.3010712E-02 energy calculations done at 7.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.320000 DelPhi exited at 04:48:28 7.319u 0.154s 0:07.97 93.6% 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 04:48:28 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 !!! 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.943771 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): -12.27800 37.20400 ymin,ymax (A): -26.02100 22.58600 zmin,zma (A): -8.918000 45.50200 x,y,z range (A): 49.48200 48.60700 54.42000 scale (grids/A): 2.943771 object centre (A): 12.46300 -1.717500 18.29200 number of atom coordinates read : 2754 total number of charged atoms : 2602 net assigned charge : 3.140012 assigned positive charge : 414.7487 centred at (gu) : 91.27077 92.71652 97.03250 assigned negative charge : -411.6093 centred at (gu) : 90.11959 91.84594 96.77975 start vw surface at 0.2200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 196070 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22934 grid for indexing accessible points = 1.400000 m= 102824 mr = 145476 m= 38820 mr = 85559 m= 9730 mr = 31903 m= 1424 mr = 7477 m= 97 mr = 969 m= 0 mr = 42 time to grow re-entrant surface = 0.8899999 no. cavity mid-points inaccessible to solvent = 4308 time to turn everything in is 1.570000 number of dielectric boundary points 77539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 20812 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) : 1.962514 object centre at (A) : 12.46300 -1.717500 18.29200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4464887 0.3397347 midg,1,midg; midg,igrid,midg -0.1254441 0.3939126 1,midg,midg; igrid,midg,midg -9.2918612E-02 0.4415832 gauss-seidel spectral radius is 0.9992798 estimated iterations to convergence 294 setup time was (sec) 1.910000 now iterating at: 04:48:30 rms-change max change #iterations 10.69671 348.9489 at 10iterations 6.292013 151.0497 at 20iterations 3.692008 81.69299 at 30iterations 2.164487 38.78032 at 40iterations 1.264271 26.65498 at 50iterations 0.7394456 13.41552 at 60iterations 0.4309575 7.908772 at 70iterations 0.2507432 4.853223 at 80iterations 0.1460405 2.529784 at 90iterations 8.4854633E-02 1.464653 at 100iterations 4.9204964E-02 0.8108177 at 110iterations 2.8602971E-02 0.4775600 at 120iterations 1.6605973E-02 0.3017902 at 130iterations 9.6299807E-03 0.1518269 at 140iterations 5.5940473E-03 8.9282990E-02 at 150iterations 3.2475526E-03 5.7394028E-02 at 160iterations 1.8844426E-03 3.1049728E-02 at 170iterations 1.0924991E-03 1.9470215E-02 at 180iterations finished qdiffx linear iterations at : 04:48:41 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 1.0924991E-03 1.9470215E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 04:48:42 12.581u 0.199s 0:13.43 95.0% 0+0k 0+0io 0pf+0w