Sat Oct 8 11:37:21 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+sph2.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 = amb2.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 11:37:21 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3336 !!! WARNING: HIR 14 has a net charge of 0.5140 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: 0.6249890 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): 31.35200 81.78300 ymin,ymax (A): 24.58000 81.54100 zmin,zma (A): -1.799000 46.89000 x,y,z range (A): 50.43101 56.96100 48.68900 scale (grids/A): 0.6249890 object centre (A): 56.56750 53.06050 22.54550 number of atom coordinates read : 3336 total number of charged atoms : 3184 net assigned charge : -5.485964 assigned positive charge : 507.3834 centred at (gu) : 90.19480 89.51626 90.73531 assigned negative charge : -512.8704 centred at (gu) : 90.02109 89.58345 90.73526 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8347 nv = 96 ne = 84 npr = 71073 no. pairs analyzed = 71073 no. exposed pairs = 3653 no. arc points = 25013 no. surface atoms = 1249 nbur = 2087 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 447 mr = 4984 m= 3 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 83 time to turn everything in is 0.3800000 number of dielectric boundary points 3720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2510 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10495 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4520996E-09 -6.0637038E-09 midg,1,midg; midg,igrid,midg 1.7824491E-09 -1.0853571E-08 1,midg,midg; igrid,midg,midg -2.2180698E-08 1.2634986E-08 gauss-seidel spectral radius is 0.9867911 estimated iterations to convergence 71 setup time was (sec) 0.6400000 now iterating at: 11:37:22 rms-change max change #iterations 0.1531698 19.69698 at 10iterations 1.4588668E-02 2.282257 at 20iterations 1.3942948E-03 0.1966171 at 30iterations 1.3872201E-04 1.8184662E-02 at 40iterations 1.8085384E-05 2.7651787E-03 at 50iterations finished qdiffx linear iterations at : 11:37:25 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 1.8085384E-05 2.7651787E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 11:37:25 3.639u 0.183s 0:04.38 86.9% 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 Sat Oct 8 2011 at 11:37:26 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3336 !!! WARNING: HIR 14 has a net charge of 0.5140 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: 1.874967 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): 31.35200 81.78300 ymin,ymax (A): 24.58000 81.54100 zmin,zma (A): -1.799000 46.89000 x,y,z range (A): 50.43101 56.96100 48.68900 scale (grids/A): 1.874967 object centre (A): 56.56750 53.06050 22.54550 number of atom coordinates read : 3336 total number of charged atoms : 3184 net assigned charge : -5.485964 assigned positive charge : 507.3834 centred at (gu) : 90.58352 88.54767 92.20489 assigned negative charge : -512.8704 centred at (gu) : 90.06270 88.74979 92.20504 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 91541 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25013 grid for indexing accessible points = 1.400000 m= 34211 mr = 66798 m= 5616 mr = 26578 m= 302 mr = 3772 m= 1 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 4193 time to turn everything in is 0.7000000 number of dielectric boundary points 34390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 24987 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) : 0.6249890 object centre at (A) : 56.56750 53.06050 22.54550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8313708E-02 -3.0934727E-02 midg,1,midg; midg,igrid,midg 2.1086020E-02 -2.1836536E-02 1,midg,midg; igrid,midg,midg -4.5666080E-02 5.5307313E-03 gauss-seidel spectral radius is 0.9986477 estimated iterations to convergence 215 setup time was (sec) 1.010000 now iterating at: 11:37:27 rms-change max change #iterations 4.816789 168.0910 at 10iterations 2.268688 66.18716 at 20iterations 1.066338 30.30730 at 30iterations 0.5024453 16.50499 at 40iterations 0.2362382 7.121888 at 50iterations 0.1113873 3.353413 at 60iterations 5.2379694E-02 1.483992 at 70iterations 2.4695393E-02 0.7042766 at 80iterations 1.1622472E-02 0.3160391 at 90iterations 5.4766033E-03 0.1741943 at 100iterations 2.5884158E-03 7.1989059E-02 at 110iterations 1.2182387E-03 3.5446167E-02 at 120iterations finished qdiffx linear iterations at : 11:37:34 total time elapsed so far: 8.060000 # loops : 120 mean,max change (kT/e) : 1.2182387E-03 3.5446167E-02 energy calculations done at 8.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 11:37:35 8.247u 0.231s 0:09.44 89.7% 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 11:37:35 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3336 !!! WARNING: HIR 14 has a net charge of 0.5140 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: 2.812451 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): 31.35200 81.78300 ymin,ymax (A): 24.58000 81.54100 zmin,zma (A): -1.799000 46.89000 x,y,z range (A): 50.43101 56.96100 48.68900 scale (grids/A): 2.812451 object centre (A): 56.56750 53.06050 22.54550 number of atom coordinates read : 3336 total number of charged atoms : 3184 net assigned charge : -5.485964 assigned positive charge : 507.3834 centred at (gu) : 90.87518 87.82138 93.30717 assigned negative charge : -512.8704 centred at (gu) : 90.09401 88.12458 93.30739 start vw surface at 0.1800000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 211852 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25013 grid for indexing accessible points = 1.400000 m= 110319 mr = 160827 m= 41426 mr = 92971 m= 10331 mr = 34920 m= 1405 mr = 8203 m= 65 mr = 993 m= 0 mr = 32 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 14054 time to turn everything in is 1.760000 number of dielectric boundary points 77452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 25471 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) : 1.874967 object centre at (A) : 56.56750 53.06050 22.54550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2176824 -0.2881623 midg,1,midg; midg,igrid,midg 0.3155382 8.9409500E-03 1,midg,midg; igrid,midg,midg -0.4889677 8.6733531E-03 gauss-seidel spectral radius is 0.9992653 estimated iterations to convergence 291 setup time was (sec) 2.100000 now iterating at: 11:37:37 rms-change max change #iterations 11.18802 373.7801 at 10iterations 6.555356 130.5591 at 20iterations 3.801567 89.54365 at 30iterations 2.208746 40.14872 at 40iterations 1.280496 21.56380 at 50iterations 0.7398027 13.21133 at 60iterations 0.4280539 7.383320 at 70iterations 0.2467614 4.314515 at 80iterations 0.1425851 2.386793 at 90iterations 8.2218260E-02 1.438858 at 100iterations 4.7466572E-02 0.7406616 at 110iterations 2.7354503E-02 0.4509220 at 120iterations 1.5764678E-02 0.2747021 at 130iterations 9.0993578E-03 0.1568699 at 140iterations 5.2489988E-03 8.3639145E-02 at 150iterations 3.0287490E-03 4.8830032E-02 at 160iterations 1.7459323E-03 2.6559830E-02 at 170iterations 1.0067757E-03 1.6790390E-02 at 180iterations finished qdiffx linear iterations at : 11:37:50 total time elapsed so far: 14.98000 # loops : 180 mean,max change (kT/e) : 1.0067757E-03 1.6790390E-02 energy calculations done at 14.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.18000 DelPhi exited at 11:37:51 15.180u 0.225s 0:15.91 96.7% 0+0k 0+0io 0pf+0w