Mon Oct 10 17:06:29 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 Mon Oct 10 2011 at 17:06:29 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 = 2589 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: 0.5568852 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): -2.251000 40.13700 ymin,ymax (A): -9.385000 41.87600 zmin,zma (A): -1.263000 62.66400 x,y,z range (A): 42.38800 51.26100 63.92700 scale (grids/A): 0.5568852 object centre (A): 18.94300 16.24550 30.70050 number of atom coordinates read : 2589 total number of charged atoms : 2453 net assigned charge : 8.000018 assigned positive charge : 380.5068 centred at (gu) : 89.46629 89.32248 89.44721 assigned negative charge : -372.5078 centred at (gu) : 89.53684 89.22076 89.49675 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5287 nv = 96 ne = 84 npr = 51304 no. pairs analyzed = 51304 no. exposed pairs = 3481 no. arc points = 24549 no. surface atoms = 1166 nbur = 1423 mkacc time = 0.1400000 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= 245 mr = 2585 m= 0 mr = 12 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2547 ## 346 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 6846 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3325150E-09 3.0446909E-10 midg,1,midg; midg,igrid,midg -1.2258201E-10 1.3522652E-09 1,midg,midg; igrid,midg,midg 1.5226557E-09 1.5049169E-10 gauss-seidel spectral radius is 0.9833432 estimated iterations to convergence 64 setup time was (sec) 0.6000000 now iterating at: 17:06:30 rms-change max change #iterations 7.3052131E-02 11.78458 at 10iterations 5.0907061E-03 1.023729 at 20iterations 3.7375369E-04 5.7579041E-02 at 30iterations 3.0348952E-05 4.9057007E-03 at 40iterations 3.1265174E-06 4.8542023E-04 at 50iterations finished qdiffx linear iterations at : 17:06:33 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 3.1265174E-06 4.8542023E-04 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 17:06:34 4.205u 0.267s 0:04.81 92.7% 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 Mon Oct 10 2011 at 17:06:34 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 = 2589 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: 1.670655 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): -2.251000 40.13700 ymin,ymax (A): -9.385000 41.87600 zmin,zma (A): -1.263000 62.66400 x,y,z range (A): 42.38800 51.26100 63.92700 scale (grids/A): 1.670655 object centre (A): 18.94300 16.24550 30.70050 number of atom coordinates read : 2589 total number of charged atoms : 2453 net assigned charge : 8.000018 assigned positive charge : 380.5068 centred at (gu) : 88.39827 87.96687 88.34119 assigned negative charge : -372.5078 centred at (gu) : 88.61040 87.66202 88.49032 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 58314 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24549 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18785 mr = 38410 m= 2107 mr = 12816 m= 58 mr = 1027 m= 1 mr = 1 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 198 time to turn everything in is 0.5200000 number of dielectric boundary points 27012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 241 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 18861 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) : 0.5568852 object centre at (A) : 18.94300 16.24550 30.70050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9682709E-02 2.2444332E-02 midg,1,midg; midg,igrid,midg -7.3365886E-03 8.9542046E-03 1,midg,midg; igrid,midg,midg 1.0695893E-02 6.4724474E-04 gauss-seidel spectral radius is 0.9982324 estimated iterations to convergence 189 setup time was (sec) 0.8600000 now iterating at: 17:06:35 rms-change max change #iterations 3.150190 155.0281 at 10iterations 1.320878 51.17966 at 20iterations 0.5558620 22.40220 at 30iterations 0.2346239 8.511450 at 40iterations 9.8579571E-02 3.710195 at 50iterations 4.1600164E-02 1.621716 at 60iterations 1.7515171E-02 0.7473660 at 70iterations 7.3881997E-03 0.2876759 at 80iterations 3.1121022E-03 0.1309052 at 90iterations 1.3118066E-03 5.0858498E-02 at 100iterations 5.5373902E-04 2.2776604E-02 at 110iterations 2.3496815E-04 9.7045898E-03 at 120iterations finished qdiffx linear iterations at : 17:06:43 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 2.3496815E-04 9.7045898E-03 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.390000 DelPhi exited at 17:06:44 9.391u 0.277s 0:09.99 96.6% 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 Mon Oct 10 2011 at 17:06:44 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 = 2589 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: 2.505983 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): -2.251000 40.13700 ymin,ymax (A): -9.385000 41.87600 zmin,zma (A): -1.263000 62.66400 x,y,z range (A): 42.38800 51.26100 63.92700 scale (grids/A): 2.505983 object centre (A): 18.94300 16.24550 30.70050 number of atom coordinates read : 2589 total number of charged atoms : 2453 net assigned charge : 8.000018 assigned positive charge : 380.5068 centred at (gu) : 87.59719 86.95012 87.51157 assigned negative charge : -372.5078 centred at (gu) : 87.91557 86.49298 87.73551 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 134947 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24549 grid for indexing accessible points = 1.400000 m= 63034 mr = 93899 m= 19333 mr = 49481 m= 3352 mr = 14454 m= 204 mr = 2125 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 650 time to turn everything in is 1.160000 number of dielectric boundary points 60851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 19606 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) : 1.670655 object centre at (A) : 18.94300 16.24550 30.70050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2302163 0.5730042 midg,1,midg; midg,igrid,midg -6.8783022E-02 0.1501394 1,midg,midg; igrid,midg,midg 0.1271650 -3.7879667E-03 gauss-seidel spectral radius is 0.9991516 estimated iterations to convergence 271 setup time was (sec) 1.490000 now iterating at: 17:06:46 rms-change max change #iterations 8.213737 319.7178 at 10iterations 4.663990 139.1117 at 20iterations 2.620047 64.55707 at 30iterations 1.462341 42.84028 at 40iterations 0.8177465 20.27759 at 50iterations 0.4546586 10.66147 at 60iterations 0.2518045 6.297975 at 70iterations 0.1397125 3.181786 at 80iterations 7.7236332E-02 1.949308 at 90iterations 4.2688612E-02 0.9975758 at 100iterations 2.3604773E-02 0.4892597 at 110iterations 1.3061108E-02 0.2902603 at 120iterations 7.2039976E-03 0.1622810 at 130iterations 3.9875577E-03 8.6975098E-02 at 140iterations 2.2007381E-03 4.7687531E-02 at 150iterations 1.2089427E-03 2.5279999E-02 at 160iterations 6.6750997E-04 1.4521837E-02 at 170iterations 3.6893858E-04 8.5315704E-03 at 180iterations finished qdiffx linear iterations at : 17:06:59 total time elapsed so far: 14.77000 # loops : 180 mean,max change (kT/e) : 3.6893858E-04 8.5315704E-03 energy calculations done at 14.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.94000 DelPhi exited at 17:06:59 14.939u 0.278s 0:15.60 97.4% 0+0k 0+0io 0pf+0w