Sat Oct 8 17:41:31 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 Sat Oct 8 2011 at 17:41:31 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3534 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5236526 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): -0.9720000 44.52400 ymin,ymax (A): -30.36800 26.16700 zmin,zma (A): 1.420000 69.40400 x,y,z range (A): 45.49600 56.53500 67.98400 scale (grids/A): 0.5236526 object centre (A): 21.77600 -2.100500 35.41200 number of atom coordinates read : 3534 total number of charged atoms : 3387 net assigned charge : -5.871980 assigned positive charge : 542.8319 centred at (gu) : 90.52518 91.74671 90.53286 assigned negative charge : -548.7059 centred at (gu) : 90.48644 91.70546 90.52922 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6122 nv = 96 ne = 84 npr = 72087 no. pairs analyzed = 72087 no. exposed pairs = 4300 no. arc points = 29242 no. surface atoms = 1464 nbur = 2070 mkacc time = 0.1800000 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 = 1.624000 m= 227 mr = 3255 m= 0 mr = 10 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2975 ## 434 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8193 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4227226E-10 -1.5728129E-10 midg,1,midg; midg,igrid,midg -1.8768105E-10 -1.0672943E-11 1,midg,midg; igrid,midg,midg -2.4782781E-10 -1.9935407E-11 gauss-seidel spectral radius is 0.9812505 estimated iterations to convergence 60 setup time was (sec) 0.6400000 now iterating at: 17:41:32 rms-change max change #iterations 6.6451982E-02 12.10142 at 10iterations 4.1359905E-03 0.6606979 at 20iterations 4.1308047E-04 6.7955017E-02 at 30iterations 9.5586423E-05 1.7638683E-02 at 40iterations 2.6457163E-05 4.7464371E-03 at 50iterations finished qdiffx linear iterations at : 17:41:36 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 2.6457163E-05 4.7464371E-03 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 17:41:36 4.568u 0.404s 0:05.23 94.8% 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 17:41:36 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3534 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.570958 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): -0.9720000 44.52400 ymin,ymax (A): -30.36800 26.16700 zmin,zma (A): 1.420000 69.40400 x,y,z range (A): 45.49600 56.53500 67.98400 scale (grids/A): 1.570958 object centre (A): 21.77600 -2.100500 35.41200 number of atom coordinates read : 3534 total number of charged atoms : 3387 net assigned charge : -5.871980 assigned positive charge : 542.8319 centred at (gu) : 91.57471 95.23916 91.59758 assigned negative charge : -548.7059 centred at (gu) : 91.45884 95.11588 91.58711 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69100 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29242 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20554 mr = 48124 m= 1801 mr = 13834 m= 32 mr = 759 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 28770 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 360 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 25589 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) : 0.5236526 object centre at (A) : 21.77600 -2.100500 35.41200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2322422E-03 1.1287690E-02 midg,1,midg; midg,igrid,midg -7.6407352E-03 -1.1036577E-02 1,midg,midg; igrid,midg,midg -4.1951123E-03 9.1098831E-04 gauss-seidel spectral radius is 0.9980753 estimated iterations to convergence 181 setup time was (sec) 0.9200000 now iterating at: 17:41:38 rms-change max change #iterations 3.428082 168.4575 at 10iterations 1.390383 66.17161 at 20iterations 0.5645769 20.53059 at 30iterations 0.2300008 8.431482 at 40iterations 9.3851738E-02 3.253378 at 50iterations 3.8392004E-02 1.486397 at 60iterations 1.5596642E-02 0.6275735 at 70iterations 6.4236405E-03 0.2679729 at 80iterations 2.6608461E-03 9.7744942E-02 at 90iterations 1.1388706E-03 4.3235779E-02 at 100iterations 5.1941792E-04 1.9633293E-02 at 110iterations 2.6078071E-04 9.3498230E-03 at 120iterations finished qdiffx linear iterations at : 17:41:47 total time elapsed so far: 10.31000 # loops : 120 mean,max change (kT/e) : 2.6078071E-04 9.3498230E-03 energy calculations done at 10.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.48000 DelPhi exited at 17:41:48 10.483u 0.446s 0:11.19 97.5% 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 Sat Oct 8 2011 at 17:41:48 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3534 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.356437 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): -0.9720000 44.52400 ymin,ymax (A): -30.36800 26.16700 zmin,zma (A): 1.420000 69.40400 x,y,z range (A): 45.49600 56.53500 67.98400 scale (grids/A): 2.356437 object centre (A): 21.77600 -2.100500 35.41200 number of atom coordinates read : 3534 total number of charged atoms : 3387 net assigned charge : -5.871980 assigned positive charge : 542.8319 centred at (gu) : 92.36185 97.85852 92.39615 assigned negative charge : -548.7059 centred at (gu) : 92.18819 97.67378 92.38065 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 161180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29242 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 73584 mr = 118096 m= 18947 mr = 58007 m= 2572 mr = 13810 m= 111 mr = 1442 m= 0 mr = 24 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.390000 number of dielectric boundary points 65015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 27044 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) : 1.570958 object centre at (A) : 21.77600 -2.100500 35.41200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2674935 7.1392953E-02 midg,1,midg; midg,igrid,midg -0.1096727 -0.1604863 1,midg,midg; igrid,midg,midg -7.5557180E-02 4.4030949E-02 gauss-seidel spectral radius is 0.9991086 estimated iterations to convergence 265 setup time was (sec) 1.710000 now iterating at: 17:41:50 rms-change max change #iterations 9.169259 298.9745 at 10iterations 5.115198 139.6301 at 20iterations 2.835669 68.74711 at 30iterations 1.562206 38.54073 at 40iterations 0.8585618 17.85415 at 50iterations 0.4687741 10.24681 at 60iterations 0.2567574 5.983727 at 70iterations 0.1401194 2.764188 at 80iterations 7.6381564E-02 1.514040 at 90iterations 4.1719310E-02 0.9055405 at 100iterations 2.2767372E-02 0.4448952 at 110iterations 1.2407160E-02 0.2509995 at 120iterations 6.7661214E-03 0.1301880 at 130iterations 3.6885743E-03 7.4834824E-02 at 140iterations 2.0147564E-03 4.2084694E-02 at 150iterations 1.1040741E-03 2.3097992E-02 at 160iterations 6.1441259E-04 1.3057709E-02 at 170iterations 3.4625470E-04 7.5128078E-03 at 180iterations finished qdiffx linear iterations at : 17:42:06 total time elapsed so far: 17.54000 # loops : 180 mean,max change (kT/e) : 3.4625470E-04 7.5128078E-03 energy calculations done at 17.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.69000 DelPhi exited at 17:42:06 17.699u 0.498s 0:18.50 98.2% 0+0k 0+0io 0pf+0w