Mon Oct 10 22:54:52 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 22:54:52 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 = 2645 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 0.6298321 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): -20.36000 31.15200 ymin,ymax (A): 20.20400 76.72700 zmin,zma (A): 9.452000 52.01700 x,y,z range (A): 51.51200 56.52299 42.56500 scale (grids/A): 0.6298321 object centre (A): 5.396001 48.46550 30.73450 number of atom coordinates read : 2645 total number of charged atoms : 2502 net assigned charge : 2.500015 assigned positive charge : 396.9927 centred at (gu) : 91.70937 88.57018 89.94250 assigned negative charge : -394.4934 centred at (gu) : 91.65257 88.91005 90.14194 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6910 nv = 96 ne = 84 npr = 53940 no. pairs analyzed = 53940 no. exposed pairs = 3085 no. arc points = 21497 no. surface atoms = 1046 nbur = 1599 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 351 mr = 3956 m= 0 mr = 40 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2059 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8446 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9810889E-08 -1.5793352E-08 midg,1,midg; midg,igrid,midg 4.3063618E-08 -2.1347478E-08 1,midg,midg; igrid,midg,midg -1.9696016E-09 1.0481621E-08 gauss-seidel spectral radius is 0.9869413 estimated iterations to convergence 72 setup time was (sec) 0.5300000 now iterating at: 22:54:53 rms-change max change #iterations 0.1374016 25.35896 at 10iterations 1.4045009E-02 2.693314 at 20iterations 1.8262947E-03 0.3876762 at 30iterations 4.5353320E-04 0.1061821 at 40iterations 1.3663096E-04 3.2867432E-02 at 50iterations finished qdiffx linear iterations at : 22:54:56 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 1.3663096E-04 3.2867432E-02 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.810000 DelPhi exited at 22:54:56 3.812u 0.408s 0:04.56 92.3% 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 22:54:56 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 = 2645 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 1.889496 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): -20.36000 31.15200 ymin,ymax (A): 20.20400 76.72700 zmin,zma (A): 9.452000 52.01700 x,y,z range (A): 51.51200 56.52299 42.56500 scale (grids/A): 1.889496 object centre (A): 5.396001 48.46550 30.73450 number of atom coordinates read : 2645 total number of charged atoms : 2502 net assigned charge : 2.500015 assigned positive charge : 396.9927 centred at (gu) : 95.12782 85.71024 89.82708 assigned negative charge : -394.4934 centred at (gu) : 94.95755 86.72984 90.42545 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75433 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21497 grid for indexing accessible points = 1.400000 m= 26721 mr = 53449 m= 4167 mr = 20191 m= 201 mr = 2718 m= 2 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2236 time to turn everything in is 0.5800000 number of dielectric boundary points 30095 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19684 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) : 0.6298321 object centre at (A) : 5.396001 48.46550 30.73450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9621350E-02 1.2077055E-03 midg,1,midg; midg,igrid,midg 1.9764734E-02 -6.1191447E-02 1,midg,midg; igrid,midg,midg -5.6947088E-03 -3.4783706E-03 gauss-seidel spectral radius is 0.9986098 estimated iterations to convergence 213 setup time was (sec) 0.8600000 now iterating at: 22:54:58 rms-change max change #iterations 4.189237 174.6482 at 10iterations 1.937862 67.90177 at 20iterations 0.9013021 26.95598 at 30iterations 0.4200265 12.77898 at 40iterations 0.1954373 5.889112 at 50iterations 9.1099083E-02 3.359512 at 60iterations 4.2475190E-02 1.470840 at 70iterations 1.9914947E-02 0.6688881 at 80iterations 9.4110882E-03 0.2825851 at 90iterations 4.5115361E-03 0.1702843 at 100iterations 2.2272575E-03 7.5920105E-02 at 110iterations 1.1494170E-03 4.5578003E-02 at 120iterations finished qdiffx linear iterations at : 22:55:06 total time elapsed so far: 8.630000 # loops : 120 mean,max change (kT/e) : 1.1494170E-03 4.5578003E-02 energy calculations done at 8.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.810000 DelPhi exited at 22:55:06 8.813u 0.446s 0:09.91 93.3% 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 22:55:06 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 = 2645 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 2.834245 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): -20.36000 31.15200 ymin,ymax (A): 20.20400 76.72700 zmin,zma (A): 9.452000 52.01700 x,y,z range (A): 51.51200 56.52299 42.56500 scale (grids/A): 2.834245 object centre (A): 5.396001 48.46550 30.73450 number of atom coordinates read : 2645 total number of charged atoms : 2502 net assigned charge : 2.500015 assigned positive charge : 396.9927 centred at (gu) : 97.69168 83.56523 89.74059 assigned negative charge : -394.4934 centred at (gu) : 97.43621 85.09472 90.63811 start vw surface at 0.1300000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 174410 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21497 grid for indexing accessible points = 1.400000 m= 88135 mr = 129234 m= 31296 mr = 73271 m= 7593 mr = 25489 m= 1003 mr = 6020 m= 52 mr = 678 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 7629 time to turn everything in is 1.520000 number of dielectric boundary points 67778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 20016 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) : 1.889496 object centre at (A) : 5.396001 48.46550 30.73450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2866503 6.0551181E-02 midg,1,midg; midg,igrid,midg -0.2581574 -0.5964506 1,midg,midg; igrid,midg,midg -0.1182720 -0.1167124 gauss-seidel spectral radius is 0.9992462 estimated iterations to convergence 287 setup time was (sec) 1.890000 now iterating at: 22:55:09 rms-change max change #iterations 9.747792 348.7339 at 10iterations 5.619899 133.1543 at 20iterations 3.237102 63.58902 at 30iterations 1.859889 42.79885 at 40iterations 1.066058 20.18856 at 50iterations 0.6105354 12.79997 at 60iterations 0.3488200 7.129335 at 70iterations 0.1998413 3.811485 at 80iterations 0.1140807 2.199081 at 90iterations 6.5384656E-02 1.173349 at 100iterations 3.7412409E-02 0.6903343 at 110iterations 2.1388639E-02 0.3744049 at 120iterations 1.2298219E-02 0.2153473 at 130iterations 7.0876903E-03 0.1305456 at 140iterations 4.1286666E-03 8.4716797E-02 at 150iterations 2.4311629E-03 5.2471161E-02 at 160iterations 1.4749191E-03 3.6899567E-02 at 170iterations 9.3568745E-04 2.2686005E-02 at 180iterations finished qdiffx linear iterations at : 22:55:22 total time elapsed so far: 14.90000 # loops : 180 mean,max change (kT/e) : 9.3568745E-04 2.2686005E-02 energy calculations done at 14.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.07000 DelPhi exited at 22:55:23 15.077u 0.458s 0:16.18 95.9% 0+0k 0+0io 0pf+0w