Tue Oct 11 06:27:50 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 Tue Oct 11 2011 at 06:27:50 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2101 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.7306461 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): 25.72100 72.37800 ymin,ymax (A): -18.67300 30.05100 zmin,zma (A): 4.154000 46.44000 x,y,z range (A): 46.65700 48.72400 42.28600 scale (grids/A): 0.7306461 object centre (A): 49.04950 5.689000 25.29700 number of atom coordinates read : 2101 total number of charged atoms : 1970 net assigned charge : 5.564012 assigned positive charge : 323.2460 centred at (gu) : 89.19167 90.50399 90.23072 assigned negative charge : -317.6821 centred at (gu) : 89.32937 90.43285 90.31933 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7645 nv = 96 ne = 84 npr = 42238 no. pairs analyzed = 42238 no. exposed pairs = 2576 no. arc points = 17604 no. surface atoms = 877 nbur = 1224 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 599 mr = 4448 m= 5 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1533 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8183 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4537417E-07 4.5051860E-09 midg,1,midg; midg,igrid,midg 1.7918653E-08 1.5116011E-07 1,midg,midg; igrid,midg,midg 2.2355447E-07 -3.1127875E-08 gauss-seidel spectral radius is 0.9902314 estimated iterations to convergence 82 setup time was (sec) 0.5100000 now iterating at: 06:27:51 rms-change max change #iterations 0.2319764 32.22889 at 10iterations 3.2004073E-02 4.064729 at 20iterations 4.8248088E-03 0.6731567 at 30iterations 9.7196142E-04 0.1085777 at 40iterations 2.9346335E-04 3.2890320E-02 at 50iterations finished qdiffx linear iterations at : 06:27:54 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 2.9346335E-04 3.2890320E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 06:27:55 3.535u 0.218s 0:04.52 82.7% 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 Tue Oct 11 2011 at 06:27:55 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2101 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.191938 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): 25.72100 72.37800 ymin,ymax (A): -18.67300 30.05100 zmin,zma (A): 4.154000 46.44000 x,y,z range (A): 46.65700 48.72400 42.28600 scale (grids/A): 2.191938 object centre (A): 49.04950 5.689000 25.29700 number of atom coordinates read : 2101 total number of charged atoms : 1970 net assigned charge : 5.564012 assigned positive charge : 323.2460 centred at (gu) : 87.57515 91.51189 90.69243 assigned negative charge : -317.6821 centred at (gu) : 87.98817 91.29856 90.95810 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 81014 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17604 grid for indexing accessible points = 1.400000 m= 34690 mr = 58102 m= 7429 mr = 26703 m= 749 mr = 5153 m= 25 mr = 387 m= 0 mr = 4 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 33558 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 15674 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) : 0.7306461 object centre at (A) : 49.04950 5.689000 25.29700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6335632E-02 2.5582880E-02 midg,1,midg; midg,igrid,midg 4.5132861E-02 3.6016971E-02 1,midg,midg; igrid,midg,midg 4.7440466E-02 -6.9064118E-02 gauss-seidel spectral radius is 0.9988951 estimated iterations to convergence 238 setup time was (sec) 1.010000 now iterating at: 06:27:56 rms-change max change #iterations 4.977278 233.9768 at 10iterations 2.510417 84.37459 at 20iterations 1.271070 44.20494 at 30iterations 0.6437213 18.11072 at 40iterations 0.3257751 9.371586 at 50iterations 0.1655210 4.540477 at 60iterations 8.3985046E-02 2.346466 at 70iterations 4.2666413E-02 1.252146 at 80iterations 2.1876233E-02 0.6119614 at 90iterations 1.1330617E-02 0.3285980 at 100iterations 5.9069400E-03 0.1656685 at 110iterations 3.1963603E-03 0.1007843 at 120iterations finished qdiffx linear iterations at : 06:28:03 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 3.1963603E-03 0.1007843 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 06:28:03 7.991u 0.205s 0:08.61 95.1% 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 Tue Oct 11 2011 at 06:28:04 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2101 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 3.287907 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): 25.72100 72.37800 ymin,ymax (A): -18.67300 30.05100 zmin,zma (A): 4.154000 46.44000 x,y,z range (A): 46.65700 48.72400 42.28600 scale (grids/A): 3.287907 object centre (A): 49.04950 5.689000 25.29700 number of atom coordinates read : 2101 total number of charged atoms : 1970 net assigned charge : 5.564012 assigned positive charge : 323.2460 centred at (gu) : 86.36269 92.26797 91.03861 assigned negative charge : -317.6821 centred at (gu) : 86.98244 91.94765 91.43723 start vw surface at 0.1600000 fill in re-entrant regions at 0.9300000 boundary points on vw surface= 186127 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17604 grid for indexing accessible points = 1.400000 m= 105776 mr = 139002 m= 46275 mr = 88917 m= 14464 mr = 38646 m= 3132 mr = 11466 m= 398 mr = 2360 m= 19 mr = 242 m= 0 mr = 7 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.110000 number of dielectric boundary points 75551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.240000 number of grid points assigned charge 15760 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) : 2.191938 object centre at (A) : 49.04950 5.689000 25.29700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1237579 0.2100361 midg,1,midg; midg,igrid,midg 0.3412406 0.1533255 1,midg,midg; igrid,midg,midg 0.4714863 -0.7902235 gauss-seidel spectral radius is 0.9993132 estimated iterations to convergence 301 setup time was (sec) 2.420000 now iterating at: 06:28:06 rms-change max change #iterations 10.88841 403.6109 at 10iterations 6.493198 174.9708 at 20iterations 3.856552 83.70938 at 30iterations 2.296292 49.49720 at 40iterations 1.362564 26.74911 at 50iterations 0.8050351 17.03681 at 60iterations 0.4762548 9.119644 at 70iterations 0.2820902 5.227285 at 80iterations 0.1664934 3.202000 at 90iterations 9.8554716E-02 1.674229 at 100iterations 5.8483653E-02 1.070477 at 110iterations 3.4964129E-02 0.6950455 at 120iterations 2.1139627E-02 0.3924122 at 130iterations 1.3101169E-02 0.2343025 at 140iterations 8.4547121E-03 0.1597137 at 150iterations 5.7410938E-03 0.1055222 at 160iterations 4.1346885E-03 8.0142975E-02 at 170iterations 3.1563605E-03 6.0134888E-02 at 180iterations finished qdiffx linear iterations at : 06:28:17 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 3.1563605E-03 6.0134888E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.14000 DelPhi exited at 06:28:17 13.146u 0.172s 0:13.72 97.0% 0+0k 0+0io 0pf+0w