Tue Oct 11 08:36:54 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 08:36:55 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2008 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 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: 0.7495526 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): -9.120000 35.17000 ymin,ymax (A): -3.624000 34.05900 zmin,zma (A): 2.104000 49.59900 x,y,z range (A): 44.29000 37.68300 47.49500 scale (grids/A): 0.7495526 object centre (A): 13.02500 15.21750 25.85150 number of atom coordinates read : 2008 total number of charged atoms : 1870 net assigned charge : 5.837007 assigned positive charge : 302.5602 centred at (gu) : 90.20190 89.53495 91.10479 assigned negative charge : -296.7232 centred at (gu) : 90.00156 89.58701 91.15639 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7848 nv = 96 ne = 84 npr = 40077 no. pairs analyzed = 40077 no. exposed pairs = 2430 no. arc points = 16712 no. surface atoms = 828 nbur = 1180 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 616 mr = 4603 m= 8 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3734 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1482 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8212 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5142022E-07 8.0848309E-08 midg,1,midg; midg,igrid,midg 2.0174625E-07 6.1627844E-08 1,midg,midg; igrid,midg,midg -1.0229622E-07 3.6383636E-07 gauss-seidel spectral radius is 0.9907080 estimated iterations to convergence 84 setup time was (sec) 0.4900000 now iterating at: 08:36:55 rms-change max change #iterations 0.2461410 34.24854 at 10iterations 3.4501072E-02 4.237373 at 20iterations 5.0127022E-03 0.7474937 at 30iterations 8.2256598E-04 9.4169617E-02 at 40iterations 1.8364251E-04 1.9161224E-02 at 50iterations finished qdiffx linear iterations at : 08:36:58 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.8364251E-04 1.9161224E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 08:36:58 3.325u 0.171s 0:03.77 92.5% 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 08:36:58 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2008 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 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: 2.248658 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): -9.120000 35.17000 ymin,ymax (A): -3.624000 34.05900 zmin,zma (A): 2.104000 49.59900 x,y,z range (A): 44.29000 37.68300 47.49500 scale (grids/A): 2.248658 object centre (A): 13.02500 15.21750 25.85150 number of atom coordinates read : 2008 total number of charged atoms : 1870 net assigned charge : 5.837007 assigned positive charge : 302.5602 centred at (gu) : 90.60577 88.60503 93.31446 assigned negative charge : -296.7232 centred at (gu) : 90.00488 88.76099 93.46950 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 82614 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16712 grid for indexing accessible points = 1.400000 m= 35657 mr = 59173 m= 7950 mr = 27781 m= 881 mr = 5558 m= 30 mr = 495 m= 0 mr = 3 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 34122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 14918 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) : 0.7495526 object centre at (A) : 13.02500 15.21750 25.85150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3822454E-02 1.3579246E-02 midg,1,midg; midg,igrid,midg 4.2844985E-02 1.1081626E-02 1,midg,midg; igrid,midg,midg 2.8707020E-02 6.7166358E-02 gauss-seidel spectral radius is 0.9989354 estimated iterations to convergence 242 setup time was (sec) 0.9500000 now iterating at: 08:36:59 rms-change max change #iterations 4.969125 177.6754 at 10iterations 2.555024 86.73686 at 20iterations 1.308390 40.63044 at 30iterations 0.6726937 21.68480 at 40iterations 0.3466734 10.16963 at 50iterations 0.1781823 5.585079 at 60iterations 9.1586746E-02 2.697037 at 70iterations 4.6890315E-02 1.294307 at 80iterations 2.4196381E-02 0.6584740 at 90iterations 1.2564309E-02 0.3507786 at 100iterations 6.5572597E-03 0.1805573 at 110iterations 3.4538647E-03 9.7015381E-02 at 120iterations finished qdiffx linear iterations at : 08:37:06 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 3.4538647E-03 9.7015381E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 08:37:07 7.646u 0.181s 0:08.26 94.6% 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 08:37:07 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2008 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 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: 3.372987 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): -9.120000 35.17000 ymin,ymax (A): -3.624000 34.05900 zmin,zma (A): 2.104000 49.59900 x,y,z range (A): 44.29000 37.68300 47.49500 scale (grids/A): 3.372987 object centre (A): 13.02500 15.21750 25.85150 number of atom coordinates read : 2008 total number of charged atoms : 1870 net assigned charge : 5.837007 assigned positive charge : 302.5602 centred at (gu) : 90.90860 87.90746 94.97179 assigned negative charge : -296.7232 centred at (gu) : 90.00747 88.14154 95.20430 start vw surface at 0.1500000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 189915 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16712 grid for indexing accessible points = 1.400000 m= 107721 mr = 141673 m= 48044 mr = 90938 m= 15531 mr = 40333 m= 3555 mr = 12409 m= 536 mr = 2633 m= 19 mr = 381 m= 0 mr = 5 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.100000 number of dielectric boundary points 76949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 14960 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) : 2.248658 object centre at (A) : 13.02500 15.21750 25.85150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4177701 4.4396657E-02 midg,1,midg; midg,igrid,midg 0.3352357 6.6628069E-02 1,midg,midg; igrid,midg,midg 0.4517433 0.4718384 gauss-seidel spectral radius is 0.9993219 estimated iterations to convergence 303 setup time was (sec) 2.400000 now iterating at: 08:37:09 rms-change max change #iterations 10.76723 261.7644 at 10iterations 6.454818 124.0135 at 20iterations 3.847308 68.05486 at 30iterations 2.292429 40.85505 at 40iterations 1.361225 24.07108 at 50iterations 0.8087527 14.95201 at 60iterations 0.4799512 8.877125 at 70iterations 0.2843701 4.630104 at 80iterations 0.1683906 2.712490 at 90iterations 9.9698648E-02 1.594599 at 100iterations 5.9199486E-02 0.9679680 at 110iterations 3.5246704E-02 0.6666613 at 120iterations 2.1106433E-02 0.3523235 at 130iterations 1.2823684E-02 0.2095375 at 140iterations 7.9965610E-03 0.1400032 at 150iterations 5.1933704E-03 9.3292236E-02 at 160iterations 3.5406742E-03 6.5528870E-02 at 170iterations 2.5733614E-03 4.2736053E-02 at 180iterations finished qdiffx linear iterations at : 08:37:20 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 2.5733614E-03 4.2736053E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.85000 DelPhi exited at 08:37:20 12.857u 0.196s 0:13.61 95.8% 0+0k 0+0io 0pf+0w