Mon Oct 10 09:44:33 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 09:44:33 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 = 2742 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5986614 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): -16.96900 36.23200 ymin,ymax (A): -64.24700 -4.781000 zmin,zma (A): -4.032000 49.01500 x,y,z range (A): 53.20100 59.46600 53.04700 scale (grids/A): 0.5986614 object centre (A): 9.631499 -34.51400 22.49150 number of atom coordinates read : 2742 total number of charged atoms : 2592 net assigned charge : 2.000010 assigned positive charge : 397.9322 centred at (gu) : 88.89236 89.50325 89.61843 assigned negative charge : -395.9324 centred at (gu) : 89.02823 89.41650 89.56323 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6651 nv = 96 ne = 84 npr = 54200 no. pairs analyzed = 54200 no. exposed pairs = 4118 no. arc points = 29563 no. surface atoms = 1363 nbur = 1379 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 2965 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 4026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2818 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8153 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3061648E-09 2.5182931E-09 midg,1,midg; midg,igrid,midg -2.6272642E-09 3.4403558E-09 1,midg,midg; igrid,midg,midg 7.1872299E-09 -3.1945064E-09 gauss-seidel spectral radius is 0.9855879 estimated iterations to convergence 68 setup time was (sec) 0.3700000 now iterating at: 09:44:33 rms-change max change #iterations 0.1084105 18.49707 at 10iterations 8.8633103E-03 1.334541 at 20iterations 7.3598692E-04 0.1202374 at 30iterations 6.5724555E-05 1.1110306E-02 at 40iterations 7.1585750E-06 1.0595322E-03 at 50iterations finished qdiffx linear iterations at : 09:44:36 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 7.1585750E-06 1.0595322E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 09:44:37 3.404u 0.214s 0:03.90 92.5% 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 09:44:37 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 = 2742 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.795984 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): -16.96900 36.23200 ymin,ymax (A): -64.24700 -4.781000 zmin,zma (A): -4.032000 49.01500 x,y,z range (A): 53.20100 59.46600 53.04700 scale (grids/A): 1.795984 object centre (A): 9.631499 -34.51400 22.49150 number of atom coordinates read : 2742 total number of charged atoms : 2592 net assigned charge : 2.000010 assigned positive charge : 397.9322 centred at (gu) : 86.67683 88.50933 88.85509 assigned negative charge : -395.9324 centred at (gu) : 87.08435 88.24927 88.68929 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29563 grid for indexing accessible points = 1.400000 m= 23120 mr = 42926 m= 3430 mr = 14735 m= 164 mr = 1578 m= 4 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 37279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 202 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 20234 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) : 0.5986614 object centre at (A) : 9.631499 -34.51400 22.49150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2477013E-03 -6.6432678E-03 midg,1,midg; midg,igrid,midg 2.1355232E-02 3.6569577E-02 1,midg,midg; igrid,midg,midg 2.2941628E-02 -7.7636559E-03 gauss-seidel spectral radius is 0.9985064 estimated iterations to convergence 205 setup time was (sec) 0.5800000 now iterating at: 09:44:38 rms-change max change #iterations 3.799779 169.3093 at 10iterations 1.707998 59.85083 at 20iterations 0.7727512 26.62441 at 30iterations 0.3487836 12.58113 at 40iterations 0.1575857 5.460911 at 50iterations 7.1417905E-02 2.591532 at 60iterations 3.2232907E-02 1.088043 at 70iterations 1.4564414E-02 0.5084152 at 80iterations 6.6060279E-03 0.2181066 at 90iterations 2.9696932E-03 0.1174545 at 100iterations 1.3426569E-03 4.7461510E-02 at 110iterations 6.0623634E-04 2.1343231E-02 at 120iterations finished qdiffx linear iterations at : 09:44:45 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 6.0623634E-04 2.1343231E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 09:44:46 7.919u 0.207s 0:08.75 92.6% 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 09:44:46 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 = 2742 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.693976 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): -16.96900 36.23200 ymin,ymax (A): -64.24700 -4.781000 zmin,zma (A): -4.032000 49.01500 x,y,z range (A): 53.20100 59.46600 53.04700 scale (grids/A): 2.693976 object centre (A): 9.631499 -34.51400 22.49150 number of atom coordinates read : 2742 total number of charged atoms : 2592 net assigned charge : 2.000010 assigned positive charge : 397.9322 centred at (gu) : 85.01528 87.76405 88.28246 assigned negative charge : -395.9324 centred at (gu) : 85.62649 87.37378 88.03375 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 161270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29563 grid for indexing accessible points = 1.400000 m= 74337 mr = 105916 m= 25741 mr = 55317 m= 5538 mr = 18518 m= 579 mr = 3260 m= 33 mr = 250 m= 0 mr = 7 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9100000 number of dielectric boundary points 84230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 20730 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) : 1.795984 object centre at (A) : 9.631499 -34.51400 22.49150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8510836E-02 -6.8689197E-02 midg,1,midg; midg,igrid,midg 0.4595195 0.5404149 1,midg,midg; igrid,midg,midg 0.2703913 -5.4900892E-02 gauss-seidel spectral radius is 0.9992524 estimated iterations to convergence 289 setup time was (sec) 1.160000 now iterating at: 09:44:47 rms-change max change #iterations 9.539693 272.1222 at 10iterations 5.667573 150.0537 at 20iterations 3.337057 95.39107 at 30iterations 1.947012 48.05315 at 40iterations 1.132513 26.11832 at 50iterations 0.6554845 15.74099 at 60iterations 0.3793621 9.097570 at 70iterations 0.2188690 4.829446 at 80iterations 0.1261402 2.793823 at 90iterations 7.2890259E-02 1.591279 at 100iterations 4.1722205E-02 0.8952560 at 110iterations 2.3992855E-02 0.6368947 at 120iterations 1.3776101E-02 0.3090634 at 130iterations 7.8914464E-03 0.1675758 at 140iterations 4.5312815E-03 9.8379612E-02 at 150iterations 2.5976540E-03 5.2305698E-02 at 160iterations 1.4904999E-03 2.8849602E-02 at 170iterations 8.5410714E-04 1.7595291E-02 at 180iterations finished qdiffx linear iterations at : 09:44:58 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 8.5410714E-04 1.7595291E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 09:44:59 12.797u 0.219s 0:13.50 96.2% 0+0k 0+0io 0pf+0w