Mon Oct 10 14:02:25 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 14:02:25 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2947 !!! WARNING: HIR 211 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6084118 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): -9.403000 43.14700 ymin,ymax (A): 25.36100 80.40200 zmin,zma (A): 100.3960 158.9090 x,y,z range (A): 52.55000 55.04100 58.51300 scale (grids/A): 0.6084118 object centre (A): 16.87200 52.88150 129.6525 number of atom coordinates read : 2947 total number of charged atoms : 2839 net assigned charge : 1.014019 assigned positive charge : 439.0539 centred at (gu) : 89.38392 89.19616 90.31412 assigned negative charge : -438.0416 centred at (gu) : 89.38232 89.07128 90.23357 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7596 nv = 96 ne = 84 npr = 56942 no. pairs analyzed = 56942 no. exposed pairs = 4190 no. arc points = 29181 no. surface atoms = 1377 nbur = 1570 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 418 mr = 3798 m= 0 mr = 40 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4176 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2906 ## 270 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9313 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4480268E-09 5.2276743E-09 midg,1,midg; midg,igrid,midg -7.3693545E-09 5.9788294E-09 1,midg,midg; igrid,midg,midg 6.1096189E-10 6.1646227E-10 gauss-seidel spectral radius is 0.9860634 estimated iterations to convergence 69 setup time was (sec) 0.5500000 now iterating at: 14:02:26 rms-change max change #iterations 0.1220761 20.22120 at 10iterations 1.0649511E-02 1.690247 at 20iterations 9.7822060E-04 0.1398315 at 30iterations 1.4009925E-04 2.2568703E-02 at 40iterations 3.8954444E-05 6.6471100E-03 at 50iterations finished qdiffx linear iterations at : 14:02:29 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 3.8954444E-05 6.6471100E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 14:02:30 3.381u 0.182s 0:05.12 69.5% 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 14:02:30 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2947 !!! WARNING: HIR 211 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: 1.825235 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): -9.403000 43.14700 ymin,ymax (A): 25.36100 80.40200 zmin,zma (A): 100.3960 158.9090 x,y,z range (A): 52.55000 55.04100 58.51300 scale (grids/A): 1.825235 object centre (A): 16.87200 52.88150 129.6525 number of atom coordinates read : 2947 total number of charged atoms : 2839 net assigned charge : 1.014019 assigned positive charge : 439.0539 centred at (gu) : 88.15086 87.58769 90.94136 assigned negative charge : -438.0416 centred at (gu) : 88.14693 87.21359 90.70022 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81304 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29181 grid for indexing accessible points = 1.400000 m= 28680 mr = 53462 m= 4601 mr = 20033 m= 264 mr = 2596 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 38695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 22233 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) : 0.6084118 object centre at (A) : 16.87200 52.88150 129.6525 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8309122E-02 -6.7521287E-03 midg,1,midg; midg,igrid,midg -9.1667706E-03 4.9419622E-03 1,midg,midg; igrid,midg,midg 1.1041294E-03 5.1740329E-03 gauss-seidel spectral radius is 0.9985815 estimated iterations to convergence 210 setup time was (sec) 0.8900000 now iterating at: 14:02:31 rms-change max change #iterations 4.215551 207.9402 at 10iterations 1.934814 78.42554 at 20iterations 0.8867720 29.88149 at 30iterations 0.4102474 12.57841 at 40iterations 0.1893965 5.910019 at 50iterations 8.7336041E-02 2.870325 at 60iterations 4.0395360E-02 1.268507 at 70iterations 1.8557953E-02 0.5947742 at 80iterations 8.6035160E-03 0.3173308 at 90iterations 3.9571114E-03 0.1608629 at 100iterations 1.8332710E-03 5.2709579E-02 at 110iterations 8.5223623E-04 2.8217316E-02 at 120iterations finished qdiffx linear iterations at : 14:02:38 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 8.5223623E-04 2.8217316E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 14:02:39 7.706u 0.230s 0:08.30 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 14:02:39 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2947 !!! WARNING: HIR 211 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.737853 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): -9.403000 43.14700 ymin,ymax (A): 25.36100 80.40200 zmin,zma (A): 100.3960 158.9090 x,y,z range (A): 52.55000 55.04100 58.51300 scale (grids/A): 2.737853 object centre (A): 16.87200 52.88150 129.6525 number of atom coordinates read : 2947 total number of charged atoms : 2839 net assigned charge : 1.014019 assigned positive charge : 439.0539 centred at (gu) : 87.22594 86.38127 91.41179 assigned negative charge : -438.0416 centred at (gu) : 87.22027 85.82037 91.05040 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 188162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29181 grid for indexing accessible points = 1.400000 m= 91900 mr = 131247 m= 33367 mr = 72061 m= 8168 mr = 25598 m= 1073 mr = 5779 m= 56 mr = 604 m= 1 mr = 18 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.450000 number of dielectric boundary points 87421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 22706 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) : 1.825235 object centre at (A) : 16.87200 52.88150 129.6525 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4505312 -0.2936507 midg,1,midg; midg,igrid,midg 8.4165307E-03 0.1057486 1,midg,midg; igrid,midg,midg 5.9622735E-02 7.8056455E-02 gauss-seidel spectral radius is 0.9992658 estimated iterations to convergence 291 setup time was (sec) 1.790000 now iterating at: 14:02:41 rms-change max change #iterations 10.32785 329.1297 at 10iterations 6.180531 168.7740 at 20iterations 3.653322 91.10894 at 30iterations 2.146098 46.68620 at 40iterations 1.255068 25.98941 at 50iterations 0.7313970 15.21330 at 60iterations 0.4255412 8.437132 at 70iterations 0.2466765 4.605456 at 80iterations 0.1429993 2.718628 at 90iterations 8.2782827E-02 1.437606 at 100iterations 4.7855668E-02 0.8771362 at 110iterations 2.7632508E-02 0.5201454 at 120iterations 1.5995149E-02 0.2823744 at 130iterations 9.2176870E-03 0.1700516 at 140iterations 5.3146607E-03 9.6385956E-02 at 150iterations 3.0783464E-03 5.2225493E-02 at 160iterations 1.7725029E-03 3.1703949E-02 at 170iterations 1.0262356E-03 1.8892288E-02 at 180iterations finished qdiffx linear iterations at : 14:02:52 total time elapsed so far: 13.01000 # loops : 180 mean,max change (kT/e) : 1.0262356E-03 1.8892288E-02 energy calculations done at 13.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 14:02:53 13.182u 0.249s 0:13.85 96.8% 0+0k 0+0io 0pf+0w