Mon Oct 10 19:32:50 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 Mon Oct 10 2011 at 19:32:50 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2938 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.6309931 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): -8.783000 47.63600 ymin,ymax (A): -6.982000 41.94600 zmin,zma (A): 0.7980000 55.51300 x,y,z range (A): 56.41900 48.92800 54.71500 scale (grids/A): 0.6309931 object centre (A): 19.42650 17.48200 28.15550 number of atom coordinates read : 2938 total number of charged atoms : 2796 net assigned charge : -2.485969 assigned positive charge : 443.3639 centred at (gu) : 89.48328 89.65519 88.71008 assigned negative charge : -445.8512 centred at (gu) : 89.46632 89.58437 88.66792 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7913 nv = 96 ne = 84 npr = 58859 no. pairs analyzed = 58859 no. exposed pairs = 3865 no. arc points = 27332 no. surface atoms = 1312 nbur = 1626 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 384 mr = 4166 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.3400000 number of dielectric boundary points 4099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2707 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9543 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.3948662E-09 1.2505941E-09 midg,1,midg; midg,igrid,midg -1.0908238E-08 4.3028616E-09 1,midg,midg; igrid,midg,midg -4.9662487E-09 -8.2582002E-10 gauss-seidel spectral radius is 0.9870255 estimated iterations to convergence 72 setup time was (sec) 0.5800000 now iterating at: 19:32:51 rms-change max change #iterations 0.1466147 21.69460 at 10iterations 1.3848231E-02 1.781935 at 20iterations 1.3608227E-03 0.1729126 at 30iterations 1.4284927E-04 1.9569397E-02 at 40iterations 2.0514168E-05 4.0340424E-03 at 50iterations finished qdiffx linear iterations at : 19:32:54 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 2.0514168E-05 4.0340424E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 19:32:55 3.568u 0.193s 0:04.23 88.6% 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 19:32:55 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2938 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.892979 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): -8.783000 47.63600 ymin,ymax (A): -6.982000 41.94600 zmin,zma (A): 0.7980000 55.51300 x,y,z range (A): 56.41900 48.92800 54.71500 scale (grids/A): 1.892979 object centre (A): 19.42650 17.48200 28.15550 number of atom coordinates read : 2938 total number of charged atoms : 2796 net assigned charge : -2.485969 assigned positive charge : 443.3639 centred at (gu) : 88.44884 88.96468 86.12961 assigned negative charge : -445.8512 centred at (gu) : 88.39868 88.75271 86.00332 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 85526 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27332 grid for indexing accessible points = 1.400000 m= 29076 mr = 58183 m= 4067 mr = 20563 m= 203 mr = 2238 m= 4 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1091 time to turn everything in is 0.6800000 number of dielectric boundary points 37845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 21971 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) : 0.6309931 object centre at (A) : 19.42650 17.48200 28.15550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6909614E-02 1.2851343E-02 midg,1,midg; midg,igrid,midg -2.0349991E-02 7.6052104E-03 1,midg,midg; igrid,midg,midg -6.2419631E-02 1.2849641E-02 gauss-seidel spectral radius is 0.9986579 estimated iterations to convergence 216 setup time was (sec) 0.9800000 now iterating at: 19:32:56 rms-change max change #iterations 4.552420 192.8264 at 10iterations 2.131909 67.71301 at 20iterations 1.005155 30.19230 at 30iterations 0.4723076 13.70061 at 40iterations 0.2228625 6.725793 at 50iterations 0.1047032 3.154137 at 60iterations 4.9314216E-02 1.411238 at 70iterations 2.3257820E-02 0.7177095 at 80iterations 1.0922654E-02 0.3229427 at 90iterations 5.1481230E-03 0.1493530 at 100iterations 2.4336218E-03 7.0068359E-02 at 110iterations 1.1475396E-03 3.2767296E-02 at 120iterations finished qdiffx linear iterations at : 19:33:04 total time elapsed so far: 8.800000 # loops : 120 mean,max change (kT/e) : 1.1475396E-03 3.2767296E-02 energy calculations done at 8.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.020000 DelPhi exited at 19:33:04 9.020u 0.223s 0:09.67 95.5% 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 Mon Oct 10 2011 at 19:33:04 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2938 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.839469 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): -8.783000 47.63600 ymin,ymax (A): -6.982000 41.94600 zmin,zma (A): 0.7980000 55.51300 x,y,z range (A): 56.41900 48.92800 54.71500 scale (grids/A): 2.839469 object centre (A): 19.42650 17.48200 28.15550 number of atom coordinates read : 2938 total number of charged atoms : 2796 net assigned charge : -2.485969 assigned positive charge : 443.3639 centred at (gu) : 87.67319 88.44697 84.19440 assigned negative charge : -445.8512 centred at (gu) : 87.59797 88.12898 84.00483 start vw surface at 0.2500000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 198060 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27332 grid for indexing accessible points = 1.400000 m= 96032 mr = 141796 m= 31988 mr = 76676 m= 6837 mr = 24699 m= 824 mr = 4705 m= 36 mr = 456 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 3531 time to turn everything in is 1.730000 number of dielectric boundary points 85436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 22361 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) : 1.892979 object centre at (A) : 19.42650 17.48200 28.15550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3692364 7.3746368E-02 midg,1,midg; midg,igrid,midg -0.2119824 7.9579704E-02 1,midg,midg; igrid,midg,midg -0.7714753 0.2947111 gauss-seidel spectral radius is 0.9992881 estimated iterations to convergence 296 setup time was (sec) 2.100000 now iterating at: 19:33:07 rms-change max change #iterations 10.89772 328.8011 at 10iterations 6.532599 163.5343 at 20iterations 3.882051 105.0970 at 30iterations 2.294559 55.47634 at 40iterations 1.348806 27.09449 at 50iterations 0.7937512 16.72592 at 60iterations 0.4635936 9.935684 at 70iterations 0.2713161 5.492748 at 80iterations 0.1582557 3.001694 at 90iterations 9.2309877E-02 1.707165 at 100iterations 5.3888861E-02 1.002220 at 110iterations 3.1360779E-02 0.6669235 at 120iterations 1.8270269E-02 0.3260679 at 130iterations 1.0638910E-02 0.1781425 at 140iterations 6.1827237E-03 0.1030057 at 150iterations 3.5978728E-03 6.5048218E-02 at 160iterations 2.0989170E-03 3.7551880E-02 at 170iterations 1.2192325E-03 2.0351171E-02 at 180iterations finished qdiffx linear iterations at : 19:33:18 total time elapsed so far: 13.77000 # loops : 180 mean,max change (kT/e) : 1.2192325E-03 2.0351171E-02 energy calculations done at 13.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.98000 DelPhi exited at 19:33:20 13.981u 0.255s 0:16.11 88.3% 0+0k 0+0io 0pf+0w