Mon Oct 10 19:55:55 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 19:55:55 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2592 !!! WARNING: HIR 105 has a net charge of 0.5140 !!! WARNING: HIR 231 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: 0.6076434 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): -12.29300 45.36900 ymin,ymax (A): -16.87700 38.37200 zmin,zma (A): -12.59400 45.99300 x,y,z range (A): 57.66200 55.24900 58.58700 scale (grids/A): 0.6076434 object centre (A): 16.53800 10.74750 16.69950 number of atom coordinates read : 2592 total number of charged atoms : 2455 net assigned charge : 1.028010 assigned positive charge : 386.6068 centred at (gu) : 89.77027 90.16179 90.15104 assigned negative charge : -385.5799 centred at (gu) : 89.74031 90.16555 90.11012 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6605 nv = 96 ne = 84 npr = 50854 no. pairs analyzed = 50854 no. exposed pairs = 3738 no. arc points = 26614 no. surface atoms = 1242 nbur = 1350 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3124 m= 2 mr = 35 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 3784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2604 ## 267 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7951 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2744248E-09 2.5153741E-09 midg,1,midg; midg,igrid,midg 7.1070427E-10 4.0540787E-10 1,midg,midg; igrid,midg,midg -8.5949592E-10 1.8354335E-09 gauss-seidel spectral radius is 0.9859958 estimated iterations to convergence 69 setup time was (sec) 0.5000000 now iterating at: 19:55:55 rms-change max change #iterations 0.1125562 17.31367 at 10iterations 9.7339824E-03 1.325455 at 20iterations 8.4849336E-04 0.1241188 at 30iterations 7.8715973E-05 1.1623383E-02 at 40iterations 8.4027579E-06 1.3122559E-03 at 50iterations finished qdiffx linear iterations at : 19:55:58 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 8.4027579E-06 1.3122559E-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) 3.450000 DelPhi exited at 19:55:59 3.457u 0.210s 0:03.97 92.1% 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 19:55:59 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2592 !!! WARNING: HIR 105 has a net charge of 0.5140 !!! WARNING: HIR 231 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: 1.822930 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): -12.29300 45.36900 ymin,ymax (A): -16.87700 38.37200 zmin,zma (A): -12.59400 45.99300 x,y,z range (A): 57.66200 55.24900 58.58700 scale (grids/A): 1.822930 object centre (A): 16.53800 10.74750 16.69950 number of atom coordinates read : 2592 total number of charged atoms : 2455 net assigned charge : 1.028010 assigned positive charge : 386.6068 centred at (gu) : 89.31037 90.48476 90.45246 assigned negative charge : -385.5799 centred at (gu) : 89.22097 90.49669 90.33042 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70368 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26614 grid for indexing accessible points = 1.400000 m= 24104 mr = 45055 m= 3674 mr = 16413 m= 187 mr = 1942 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 34882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19205 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) : 0.6076434 object centre at (A) : 16.53800 10.74750 16.69950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5868089E-03 -1.2572379E-02 midg,1,midg; midg,igrid,midg 1.7095447E-02 5.1006796E-03 1,midg,midg; igrid,midg,midg 1.3586118E-02 4.6760929E-03 gauss-seidel spectral radius is 0.9985397 estimated iterations to convergence 207 setup time was (sec) 0.8400000 now iterating at: 19:56:00 rms-change max change #iterations 3.907283 181.2263 at 10iterations 1.768975 67.64314 at 20iterations 0.8045411 28.58159 at 30iterations 0.3664976 12.31756 at 40iterations 0.1666426 5.952290 at 50iterations 7.5731531E-02 2.478884 at 60iterations 3.4538567E-02 1.303587 at 70iterations 1.5747737E-02 0.5115137 at 80iterations 7.1814288E-03 0.2401505 at 90iterations 3.2864157E-03 0.1090100 at 100iterations 1.4944186E-03 4.9682617E-02 at 110iterations 6.8359147E-04 2.2878647E-02 at 120iterations finished qdiffx linear iterations at : 19:56:06 total time elapsed so far: 7.210000 # loops : 120 mean,max change (kT/e) : 6.8359147E-04 2.2878647E-02 energy calculations done at 7.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 19:56:07 7.380u 0.234s 0:07.99 95.2% 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 19:56:07 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2592 !!! WARNING: HIR 105 has a net charge of 0.5140 !!! WARNING: HIR 231 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.734395 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): -12.29300 45.36900 ymin,ymax (A): -16.87700 38.37200 zmin,zma (A): -12.59400 45.99300 x,y,z range (A): 57.66200 55.24900 58.58700 scale (grids/A): 2.734395 object centre (A): 16.53800 10.74750 16.69950 number of atom coordinates read : 2592 total number of charged atoms : 2455 net assigned charge : 1.028010 assigned positive charge : 386.6068 centred at (gu) : 88.96539 90.72688 90.67867 assigned negative charge : -385.5799 centred at (gu) : 88.83146 90.74500 90.49564 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 162503 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26614 grid for indexing accessible points = 1.400000 m= 77349 mr = 110243 m= 27594 mr = 60120 m= 6292 mr = 20868 m= 714 mr = 4181 m= 28 mr = 373 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 78695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 19636 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) : 1.822930 object centre at (A) : 16.53800 10.74750 16.69950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7170243E-02 -0.1177768 midg,1,midg; midg,igrid,midg 0.2722686 6.9223434E-02 1,midg,midg; igrid,midg,midg 0.2174456 3.4188613E-02 gauss-seidel spectral radius is 0.9992471 estimated iterations to convergence 288 setup time was (sec) 1.630000 now iterating at: 19:56:09 rms-change max change #iterations 9.654689 325.2983 at 10iterations 5.720438 186.3109 at 20iterations 3.348235 77.00419 at 30iterations 1.949418 44.21194 at 40iterations 1.132763 21.95439 at 50iterations 0.6530734 15.43221 at 60iterations 0.3768165 9.182364 at 70iterations 0.2165014 4.417679 at 80iterations 0.1243254 2.503494 at 90iterations 7.1486712E-02 1.351015 at 100iterations 4.0878579E-02 0.7808948 at 110iterations 2.3456689E-02 0.4515152 at 120iterations 1.3431534E-02 0.2603836 at 130iterations 7.6697292E-03 0.1443300 at 140iterations 4.3954006E-03 8.1919670E-02 at 150iterations 2.5175277E-03 5.0123215E-02 at 160iterations 1.4419998E-03 2.9102325E-02 at 170iterations 8.2912779E-04 1.7337799E-02 at 180iterations finished qdiffx linear iterations at : 19:56:20 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 8.2912779E-04 1.7337799E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 19:56:20 12.925u 0.234s 0:13.55 97.0% 0+0k 0+0io 0pf+0w