Sat Oct 8 14:10:52 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 8 2011 at 14:10:53 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2925 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 0.6395171 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): -11.33300 44.33400 ymin,ymax (A): 10.69000 54.73700 zmin,zma (A): 41.43200 94.31700 x,y,z range (A): 55.66700 44.04700 52.88500 scale (grids/A): 0.6395171 object centre (A): 16.50050 32.71350 67.87450 number of atom coordinates read : 2925 total number of charged atoms : 2781 net assigned charge : -0.9999929 assigned positive charge : 437.2217 centred at (gu) : 88.88808 89.57533 90.21848 assigned negative charge : -438.2225 centred at (gu) : 88.86066 89.50235 90.18685 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8063 nv = 96 ne = 84 npr = 61144 no. pairs analyzed = 61144 no. exposed pairs = 3375 no. arc points = 23342 no. surface atoms = 1158 nbur = 1767 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 416 mr = 4744 m= 4 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2246 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9678 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2203291E-09 2.8805036E-09 midg,1,midg; midg,igrid,midg -1.1956686E-08 7.3318303E-09 1,midg,midg; igrid,midg,midg -6.2609553E-09 1.7129835E-09 gauss-seidel spectral radius is 0.9873554 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 14:10:53 rms-change max change #iterations 0.1570525 21.08334 at 10iterations 1.5793310E-02 2.012764 at 20iterations 1.7005706E-03 0.2425804 at 30iterations 2.4733244E-04 3.5686493E-02 at 40iterations 5.0209728E-05 7.6446533E-03 at 50iterations finished qdiffx linear iterations at : 14:10:56 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 5.0209728E-05 7.6446533E-03 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 14:10:56 3.227u 0.158s 0:03.78 89.1% 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 Sat Oct 8 2011 at 14:10:56 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2925 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 1.918551 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): -11.33300 44.33400 ymin,ymax (A): 10.69000 54.73700 zmin,zma (A): 41.43200 94.31700 x,y,z range (A): 55.66700 44.04700 52.88500 scale (grids/A): 1.918551 object centre (A): 16.50050 32.71350 67.87450 number of atom coordinates read : 2925 total number of charged atoms : 2781 net assigned charge : -0.9999929 assigned positive charge : 437.2217 centred at (gu) : 86.66360 88.72502 90.65485 assigned negative charge : -438.2225 centred at (gu) : 86.58195 88.50700 90.56009 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 87446 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23342 grid for indexing accessible points = 1.400000 m= 32579 mr = 63400 m= 5044 mr = 24753 m= 249 mr = 3091 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 34003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 21892 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) : 0.6395171 object centre at (A) : 16.50050 32.71350 67.87450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3372269E-02 5.2225110E-03 midg,1,midg; midg,igrid,midg -3.8499415E-03 1.3902022E-02 1,midg,midg; igrid,midg,midg -1.9000273E-02 1.6092369E-02 gauss-seidel spectral radius is 0.9986800 estimated iterations to convergence 218 setup time was (sec) 0.8500000 now iterating at: 14:10:57 rms-change max change #iterations 4.635022 223.6451 at 10iterations 2.212309 78.41690 at 20iterations 1.050151 32.80313 at 30iterations 0.4975531 14.27800 at 40iterations 0.2362433 7.123726 at 50iterations 0.1126053 3.094307 at 60iterations 5.3538892E-02 1.552124 at 70iterations 2.5435671E-02 0.7535248 at 80iterations 1.2084671E-02 0.3606262 at 90iterations 5.7788030E-03 0.1708221 at 100iterations 2.7521129E-03 7.6923370E-02 at 110iterations 1.3150437E-03 3.7334442E-02 at 120iterations finished qdiffx linear iterations at : 14:11:03 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 1.3150437E-03 3.7334442E-02 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.120000 DelPhi exited at 14:11:04 7.122u 0.172s 0:07.62 95.6% 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 Sat Oct 8 2011 at 14:11:04 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2925 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.877827 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): -11.33300 44.33400 ymin,ymax (A): 10.69000 54.73700 zmin,zma (A): 41.43200 94.31700 x,y,z range (A): 55.66700 44.04700 52.88500 scale (grids/A): 2.877827 object centre (A): 16.50050 32.71350 67.87450 number of atom coordinates read : 2925 total number of charged atoms : 2781 net assigned charge : -0.9999929 assigned positive charge : 437.2217 centred at (gu) : 84.99520 88.08738 90.98209 assigned negative charge : -438.2225 centred at (gu) : 84.87277 87.76038 90.84007 start vw surface at 0.1800000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 202315 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23342 grid for indexing accessible points = 1.400000 m= 105868 mr = 153058 m= 38517 mr = 88514 m= 9119 mr = 31303 m= 1197 mr = 6676 m= 46 mr = 798 m= 0 mr = 4 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.570000 number of dielectric boundary points 76709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 22248 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) : 1.918551 object centre at (A) : 16.50050 32.71350 67.87450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0229725E-03 0.1137393 midg,1,midg; midg,igrid,midg -1.2290178E-02 0.1324091 1,midg,midg; igrid,midg,midg -0.1001284 0.4125368 gauss-seidel spectral radius is 0.9992722 estimated iterations to convergence 293 setup time was (sec) 1.860000 now iterating at: 14:11:06 rms-change max change #iterations 10.81837 398.0911 at 10iterations 6.392081 141.1254 at 20iterations 3.751837 74.67712 at 30iterations 2.196608 50.46941 at 40iterations 1.280332 24.62355 at 50iterations 0.7467300 12.51678 at 60iterations 0.4334564 8.999039 at 70iterations 0.2520011 4.650339 at 80iterations 0.1459627 2.766258 at 90iterations 8.4683284E-02 1.453707 at 100iterations 4.9119480E-02 0.9146061 at 110iterations 2.8431736E-02 0.5773547 at 120iterations 1.6471658E-02 0.2699890 at 130iterations 9.5549878E-03 0.1571522 at 140iterations 5.5663679E-03 9.3238831E-02 at 150iterations 3.2503163E-03 5.3655624E-02 at 160iterations 1.9113407E-03 3.1177521E-02 at 170iterations 1.1374529E-03 1.7784119E-02 at 180iterations finished qdiffx linear iterations at : 14:11:16 total time elapsed so far: 11.41000 # loops : 180 mean,max change (kT/e) : 1.1374529E-03 1.7784119E-02 energy calculations done at 11.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.60000 DelPhi exited at 14:11:16 11.599u 0.185s 0:12.07 97.5% 0+0k 0+0io 0pf+0w