Sat Oct 8 11:40:56 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 11:40:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5599861 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): -28.11300 35.46000 ymin,ymax (A): 37.34900 95.05800 zmin,zma (A): 30.42300 89.42200 x,y,z range (A): 63.57301 57.70900 58.99899 scale (grids/A): 0.5599861 object centre (A): 3.673501 66.20350 59.92250 number of atom coordinates read : 4340 total number of charged atoms : 4182 net assigned charge : -0.4999618 assigned positive charge : 654.1041 centred at (gu) : 91.20979 88.13455 89.25032 assigned negative charge : -654.6075 centred at (gu) : 91.05722 88.26060 89.44275 start vw surface at 0.2100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8435 nv = 96 ne = 84 npr = 92712 no. pairs analyzed = 92712 no. exposed pairs = 4820 no. arc points = 32298 no. surface atoms = 1643 nbur = 2697 mkacc time = 0.3200000 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 = 1.540000 m= 326 mr = 4881 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 146 time to turn everything in is 0.6200000 number of dielectric boundary points 3860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3444 ## 434 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 11369 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4907661E-09 -2.7845857E-09 midg,1,midg; midg,igrid,midg 2.9677401E-09 -1.4140387E-09 1,midg,midg; igrid,midg,midg -1.9878450E-09 3.0783465E-09 gauss-seidel spectral radius is 0.9836392 estimated iterations to convergence 64 setup time was (sec) 0.9300000 now iterating at: 11:40:58 rms-change max change #iterations 0.1038003 16.02086 at 10iterations 7.6766349E-03 1.028994 at 20iterations 6.5136008E-04 9.1140747E-02 at 30iterations 1.2574733E-04 2.1447182E-02 at 40iterations 4.6557212E-05 7.2383881E-03 at 50iterations finished qdiffx linear iterations at : 11:41:02 total time elapsed so far: 5.020000 # loops : 50 mean,max change (kT/e) : 4.6557212E-05 7.2383881E-03 energy calculations done at 5.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.230000 DelPhi exited at 11:41:02 5.239u 0.428s 0:05.96 94.7% 0+0k 0+0io 5pf+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 11:41:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.679958 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): -28.11300 35.46000 ymin,ymax (A): 37.34900 95.05800 zmin,zma (A): 30.42300 89.42200 x,y,z range (A): 63.57301 57.70900 58.99899 scale (grids/A): 1.679958 object centre (A): 3.673501 66.20350 59.92250 number of atom coordinates read : 4340 total number of charged atoms : 4182 net assigned charge : -0.4999618 assigned positive charge : 654.1041 centred at (gu) : 93.62799 84.40229 87.74949 assigned negative charge : -654.6075 centred at (gu) : 93.17107 84.78130 88.32776 start vw surface at 0.2200000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 93871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32298 grid for indexing accessible points = 1.400000 m= 31396 mr = 67751 m= 3522 mr = 23145 m= 95 mr = 2005 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 8467 time to turn everything in is 0.9700000 number of dielectric boundary points 35976 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 389 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 32268 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) : 0.5599861 object centre at (A) : 3.673501 66.20350 59.92250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5456769E-02 -2.7605217E-02 midg,1,midg; midg,igrid,midg 3.0096466E-02 -1.2565841E-02 1,midg,midg; igrid,midg,midg -2.0239765E-02 3.7584528E-02 gauss-seidel spectral radius is 0.9983981 estimated iterations to convergence 198 setup time was (sec) 1.320000 now iterating at: 11:41:04 rms-change max change #iterations 4.407112 169.7664 at 10iterations 1.937426 60.21872 at 20iterations 0.8563269 25.24947 at 30iterations 0.3776637 10.78613 at 40iterations 0.1661780 4.895396 at 50iterations 7.3345266E-02 2.189147 at 60iterations 3.2345701E-02 0.9469271 at 70iterations 1.4251159E-02 0.4399128 at 80iterations 6.3098674E-03 0.2168961 at 90iterations 2.8013024E-03 8.2104683E-02 at 100iterations 1.2553784E-03 3.8986206E-02 at 110iterations 5.7737558E-04 1.7548084E-02 at 120iterations finished qdiffx linear iterations at : 11:41:15 total time elapsed so far: 11.90000 # loops : 120 mean,max change (kT/e) : 5.7737558E-04 1.7548084E-02 energy calculations done at 11.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.14000 DelPhi exited at 11:41:15 12.141u 0.487s 0:12.92 97.6% 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 11:41:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.519938 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): -28.11300 35.46000 ymin,ymax (A): 37.34900 95.05800 zmin,zma (A): 30.42300 89.42200 x,y,z range (A): 63.57301 57.70900 58.99899 scale (grids/A): 2.519938 object centre (A): 3.673501 66.20350 59.92250 number of atom coordinates read : 4340 total number of charged atoms : 4182 net assigned charge : -0.4999618 assigned positive charge : 654.1041 centred at (gu) : 95.44158 81.60319 86.62397 assigned negative charge : -654.6075 centred at (gu) : 94.75662 82.17178 87.49153 start vw surface at 0.2200000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 218308 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32298 grid for indexing accessible points = 1.400000 m= 106876 mr = 164549 m= 32915 mr = 88084 m= 5747 mr = 26246 m= 439 mr = 4091 m= 9 mr = 205 m= 0 mr = 0 time to grow re-entrant surface = 1.450000 no. cavity mid-points inaccessible to solvent = 27784 time to turn everything in is 2.430000 number of dielectric boundary points 81119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 2.610000 number of grid points assigned charge 33437 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) : 1.679958 object centre at (A) : 3.673501 66.20350 59.92250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5231615 -0.3592278 midg,1,midg; midg,igrid,midg 0.3943286 -0.2741417 1,midg,midg; igrid,midg,midg -0.2238668 0.4048415 gauss-seidel spectral radius is 0.9992159 estimated iterations to convergence 282 setup time was (sec) 2.830000 now iterating at: 11:41:18 rms-change max change #iterations 10.99581 339.3450 at 10iterations 6.309442 137.9033 at 20iterations 3.613306 70.96710 at 30iterations 2.058481 44.05853 at 40iterations 1.175498 21.53132 at 50iterations 0.6675807 12.24501 at 60iterations 0.3792565 7.108330 at 70iterations 0.2152222 3.958888 at 80iterations 0.1220992 1.988393 at 90iterations 6.9175683E-02 1.125589 at 100iterations 3.9183002E-02 0.6683254 at 110iterations 2.2219980E-02 0.4277096 at 120iterations 1.2597198E-02 0.2183437 at 130iterations 7.1433973E-03 0.1303778 at 140iterations 4.0492900E-03 7.9456329E-02 at 150iterations 2.3024089E-03 3.8809776E-02 at 160iterations 1.3137932E-03 2.1459579E-02 at 170iterations 7.5593614E-04 1.4099121E-02 at 180iterations finished qdiffx linear iterations at : 11:41:36 total time elapsed so far: 20.64000 # loops : 180 mean,max change (kT/e) : 7.5593614E-04 1.4099121E-02 energy calculations done at 20.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.86000 DelPhi exited at 11:41:37 20.868u 0.513s 0:21.75 98.2% 0+0k 0+0io 0pf+0w