Mon Oct 10 09:45:45 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 Mon Oct 10 2011 at 09:45:45 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2816 !!! WARNING: HIT 232 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5805137 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): -17.76100 36.15500 ymin,ymax (A): -64.96300 -4.545000 zmin,zma (A): -3.339000 57.98600 x,y,z range (A): 53.91600 60.41800 61.32500 scale (grids/A): 0.5805137 object centre (A): 9.197000 -34.75400 27.32350 number of atom coordinates read : 2816 total number of charged atoms : 2667 net assigned charge : 7.014018 assigned positive charge : 415.1289 centred at (gu) : 89.23186 89.45130 87.60185 assigned negative charge : -408.1154 centred at (gu) : 89.37241 89.32162 87.44740 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6549 nv = 96 ne = 84 npr = 53841 no. pairs analyzed = 53841 no. exposed pairs = 4143 no. arc points = 30579 no. surface atoms = 1373 nbur = 1443 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 307 mr = 2922 m= 0 mr = 12 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3922 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3097 ## 328 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8169 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8943148E-09 2.7146154E-09 midg,1,midg; midg,igrid,midg -1.2116019E-09 3.7257366E-09 1,midg,midg; igrid,midg,midg 5.3284763E-09 -1.0557345E-09 gauss-seidel spectral radius is 0.9846909 estimated iterations to convergence 66 setup time was (sec) 0.6300000 now iterating at: 09:45:46 rms-change max change #iterations 9.4856560E-02 17.71423 at 10iterations 7.1637863E-03 1.062223 at 20iterations 5.7852495E-04 8.1203461E-02 at 30iterations 4.8386763E-05 8.3532333E-03 at 40iterations 5.4891593E-06 7.4768066E-04 at 50iterations finished qdiffx linear iterations at : 09:45:50 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 5.4891593E-06 7.4768066E-04 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 09:45:50 4.485u 0.391s 0:05.24 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 09:45:51 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2816 !!! WARNING: HIT 232 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.741541 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): -17.76100 36.15500 ymin,ymax (A): -64.96300 -4.545000 zmin,zma (A): -3.339000 57.98600 x,y,z range (A): 53.91600 60.41800 61.32500 scale (grids/A): 1.741541 object centre (A): 9.197000 -34.75400 27.32350 number of atom coordinates read : 2816 total number of charged atoms : 2667 net assigned charge : 7.014018 assigned positive charge : 415.1289 centred at (gu) : 87.69521 88.35327 82.80563 assigned negative charge : -408.1154 centred at (gu) : 88.11692 87.96463 82.34177 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69529 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30579 grid for indexing accessible points = 1.400000 m= 21892 mr = 42718 m= 2874 mr = 14024 m= 122 mr = 1345 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 151 time to turn everything in is 0.6100000 number of dielectric boundary points 36309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 20762 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) : 0.5805137 object centre at (A) : 9.197000 -34.75400 27.32350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4221146E-03 1.6267495E-02 midg,1,midg; midg,igrid,midg 2.5822097E-02 3.8937930E-02 1,midg,midg; igrid,midg,midg 1.5854787E-02 1.8417942E-03 gauss-seidel spectral radius is 0.9984189 estimated iterations to convergence 200 setup time was (sec) 0.9400000 now iterating at: 09:45:52 rms-change max change #iterations 3.690996 156.7148 at 10iterations 1.625056 74.61927 at 20iterations 0.7141297 25.21951 at 30iterations 0.3133151 11.68452 at 40iterations 0.1376887 4.543900 at 50iterations 6.0873035E-02 2.071960 at 60iterations 2.6821161E-02 0.9256530 at 70iterations 1.1857483E-02 0.4301758 at 80iterations 5.2017299E-03 0.1940041 at 90iterations 2.2968911E-03 8.5324287E-02 at 100iterations 1.0099176E-03 3.5018921E-02 at 110iterations 4.4602691E-04 1.4663696E-02 at 120iterations finished qdiffx linear iterations at : 09:46:01 total time elapsed so far: 10.53000 # loops : 120 mean,max change (kT/e) : 4.4602691E-04 1.4663696E-02 energy calculations done at 10.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.69000 DelPhi exited at 09:46:02 10.696u 0.441s 0:11.47 97.0% 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 09:46:02 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2816 !!! WARNING: HIT 232 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.612311 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): -17.76100 36.15500 ymin,ymax (A): -64.96300 -4.545000 zmin,zma (A): -3.339000 57.98600 x,y,z range (A): 53.91600 60.41800 61.32500 scale (grids/A): 2.612311 object centre (A): 9.197000 -34.75400 27.32350 number of atom coordinates read : 2816 total number of charged atoms : 2667 net assigned charge : 7.014018 assigned positive charge : 415.1289 centred at (gu) : 86.54264 87.52993 79.20819 assigned negative charge : -408.1154 centred at (gu) : 87.17535 86.94688 78.51267 start vw surface at 0.1200000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 160945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30579 grid for indexing accessible points = 1.400000 m= 72173 mr = 105548 m= 23359 mr = 54094 m= 4609 mr = 16830 m= 488 mr = 2783 m= 18 mr = 264 m= 0 mr = 4 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 531 time to turn everything in is 1.490000 number of dielectric boundary points 82069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 21325 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) : 1.741541 object centre at (A) : 9.197000 -34.75400 27.32350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1209124 0.1797795 midg,1,midg; midg,igrid,midg 0.6685618 0.5132647 1,midg,midg; igrid,midg,midg 0.1225851 6.2520884E-02 gauss-seidel spectral radius is 0.9992239 estimated iterations to convergence 283 setup time was (sec) 1.870000 now iterating at: 09:46:04 rms-change max change #iterations 9.424838 298.7802 at 10iterations 5.568119 163.5813 at 20iterations 3.245051 90.07095 at 30iterations 1.873712 51.42126 at 40iterations 1.078641 29.27480 at 50iterations 0.6186588 14.65827 at 60iterations 0.3534699 7.769849 at 70iterations 0.2025622 4.262123 at 80iterations 0.1151981 2.317703 at 90iterations 6.5593086E-02 1.503189 at 100iterations 3.7368689E-02 0.8755569 at 110iterations 2.1231839E-02 0.4502597 at 120iterations 1.2062288E-02 0.2738829 at 130iterations 6.8462645E-03 0.1538320 at 140iterations 3.8847134E-03 8.0375671E-02 at 150iterations 2.2028275E-03 4.8078060E-02 at 160iterations 1.2464654E-03 2.3303986E-02 at 170iterations 7.0742238E-04 1.3442993E-02 at 180iterations finished qdiffx linear iterations at : 09:46:20 total time elapsed so far: 17.85000 # loops : 180 mean,max change (kT/e) : 7.0742238E-04 1.3442993E-02 energy calculations done at 17.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.01000 DelPhi exited at 09:46:21 18.017u 0.470s 0:18.76 98.5% 0+0k 0+0io 0pf+0w