Mon Oct 10 13:59:31 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 Mon Oct 10 2011 at 13:59:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2325 !!! WARNING: HIR 537 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6304678 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): -6.596000 44.09500 ymin,ymax (A): -12.69900 43.76700 zmin,zma (A): -13.49800 30.28700 x,y,z range (A): 50.69100 56.46600 43.78500 scale (grids/A): 0.6304678 object centre (A): 18.74950 15.53400 8.394501 number of atom coordinates read : 2325 total number of charged atoms : 2181 net assigned charge : 1.514007 assigned positive charge : 351.2075 centred at (gu) : 90.17099 89.98394 89.04478 assigned negative charge : -349.6940 centred at (gu) : 90.25122 89.88026 89.00664 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6456 nv = 96 ne = 84 npr = 43120 no. pairs analyzed = 43120 no. exposed pairs = 3491 no. arc points = 24713 no. surface atoms = 1155 nbur = 1170 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 3069 m= 4 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2354 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7534 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7162164E-09 3.8967847E-09 midg,1,midg; midg,igrid,midg -6.7656298E-09 9.9610649E-09 1,midg,midg; igrid,midg,midg 7.8428766E-09 -4.9989337E-09 gauss-seidel spectral radius is 0.9869608 estimated iterations to convergence 72 setup time was (sec) 0.5100000 now iterating at: 13:59:32 rms-change max change #iterations 0.1301176 20.84464 at 10iterations 1.2179005E-02 1.730717 at 20iterations 1.1547134E-03 0.1785774 at 30iterations 1.2039632E-04 2.0413101E-02 at 40iterations 1.9012428E-05 3.7429333E-03 at 50iterations finished qdiffx linear iterations at : 13:59:35 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.9012428E-05 3.7429333E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 13:59:36 3.538u 0.161s 0:04.69 78.6% 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 13:59:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2325 !!! WARNING: HIR 537 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.891404 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): -6.596000 44.09500 ymin,ymax (A): -12.69900 43.76700 zmin,zma (A): -13.49800 30.28700 x,y,z range (A): 50.69100 56.46600 43.78500 scale (grids/A): 1.891404 object centre (A): 18.74950 15.53400 8.394501 number of atom coordinates read : 2325 total number of charged atoms : 2181 net assigned charge : 1.514007 assigned positive charge : 351.2075 centred at (gu) : 90.51265 89.95171 87.13414 assigned negative charge : -349.6940 centred at (gu) : 90.75356 89.64082 87.01993 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 68376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24713 grid for indexing accessible points = 1.400000 m= 24613 mr = 43529 m= 4109 mr = 16731 m= 221 mr = 2287 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 34728 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 17100 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) : 0.6304678 object centre at (A) : 18.74950 15.53400 8.394501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6508313E-03 4.9107736E-03 midg,1,midg; midg,igrid,midg -2.9261764E-02 1.4874051E-02 1,midg,midg; igrid,midg,midg 1.6347194E-02 1.4721433E-03 gauss-seidel spectral radius is 0.9986159 estimated iterations to convergence 213 setup time was (sec) 0.9300000 now iterating at: 13:59:37 rms-change max change #iterations 3.992499 195.2619 at 10iterations 1.863305 67.60825 at 20iterations 0.8652221 32.92812 at 30iterations 0.4009911 14.73900 at 40iterations 0.1859970 6.827721 at 50iterations 8.6596534E-02 3.661781 at 60iterations 4.0278535E-02 1.272034 at 70iterations 1.8732047E-02 0.5865850 at 80iterations 8.7033352E-03 0.3091278 at 90iterations 4.0613147E-03 0.1355057 at 100iterations 1.8826199E-03 6.3491821E-02 at 110iterations 8.8269782E-04 2.9651642E-02 at 120iterations finished qdiffx linear iterations at : 13:59:44 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 8.8269782E-04 2.9651642E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 13:59:44 7.630u 0.184s 0:08.34 93.6% 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 13:59:44 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 = 2325 !!! WARNING: HIR 537 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: 2.837105 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): -6.596000 44.09500 ymin,ymax (A): -12.69900 43.76700 zmin,zma (A): -13.49800 30.28700 x,y,z range (A): 50.69100 56.46600 43.78500 scale (grids/A): 2.837105 object centre (A): 18.74950 15.53400 8.394501 number of atom coordinates read : 2325 total number of charged atoms : 2181 net assigned charge : 1.514007 assigned positive charge : 351.2075 centred at (gu) : 90.76888 89.92751 85.70114 assigned negative charge : -349.6940 centred at (gu) : 91.13033 89.46120 85.52995 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 157505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24713 grid for indexing accessible points = 1.400000 m= 77229 mr = 106587 m= 29094 mr = 59724 m= 7311 mr = 22000 m= 949 mr = 5010 m= 52 mr = 513 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.390000 number of dielectric boundary points 78292 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 17447 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) : 1.891404 object centre at (A) : 18.74950 15.53400 8.394501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7881515E-02 7.1380526E-02 midg,1,midg; midg,igrid,midg -0.1511797 0.3998049 1,midg,midg; igrid,midg,midg 0.2385117 -1.2832605E-02 gauss-seidel spectral radius is 0.9992734 estimated iterations to convergence 293 setup time was (sec) 1.700000 now iterating at: 13:59:46 rms-change max change #iterations 9.710481 409.5046 at 10iterations 5.823907 123.7350 at 20iterations 3.442062 72.99760 at 30iterations 2.025734 43.78704 at 40iterations 1.186383 27.01688 at 50iterations 0.6942720 14.86731 at 60iterations 0.4041988 7.972351 at 70iterations 0.2354872 4.488808 at 80iterations 0.1365312 2.737545 at 90iterations 7.9206556E-02 1.879287 at 100iterations 4.5869354E-02 0.9133377 at 110iterations 2.6542354E-02 0.5219879 at 120iterations 1.5345076E-02 0.2970047 at 130iterations 8.9126593E-03 0.1800020 at 140iterations 5.1427730E-03 9.9487305E-02 at 150iterations 2.9761167E-03 5.8613777E-02 at 160iterations 1.7223696E-03 3.7025452E-02 at 170iterations 9.9926093E-04 1.7941475E-02 at 180iterations finished qdiffx linear iterations at : 13:59:57 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 9.9926093E-04 1.7941475E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 13:59:58 12.911u 0.178s 0:13.94 93.8% 0+0k 0+0io 0pf+0w