Sun Oct 9 19:31:16 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 Sun Oct 9 2011 at 19:31:16 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5531 !!! WARNING: ASL 282 has a net charge of -0.1000 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5028178 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): 3.140000 68.16600 ymin,ymax (A): -9.029000 53.44300 zmin,zma (A): -2.056000 68.74500 x,y,z range (A): 65.02600 62.47200 70.80099 scale (grids/A): 0.5028178 object centre (A): 35.65300 22.20700 33.34450 number of atom coordinates read : 5531 total number of charged atoms : 5353 net assigned charge : 4.668028 assigned positive charge : 849.5988 centred at (gu) : 88.45152 89.33722 88.91690 assigned negative charge : -844.9370 centred at (gu) : 88.38995 89.37057 88.85181 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8933 nv = 96 ne = 84 npr = 112391 no. pairs analyzed = 112391 no. exposed pairs = 6417 no. arc points = 43658 no. surface atoms = 2177 nbur = 3354 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 297 mr = 4949 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4377 ## 641 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 11993 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2594603E-10 1.4261929E-10 midg,1,midg; midg,igrid,midg 1.4595225E-10 -1.8955268E-11 1,midg,midg; igrid,midg,midg -1.3172662E-10 1.2115942E-10 gauss-seidel spectral radius is 0.9798225 estimated iterations to convergence 58 setup time was (sec) 0.5500000 now iterating at: 19:31:17 rms-change max change #iterations 7.4951157E-02 11.66658 at 10iterations 1.0252625E-02 1.583332 at 20iterations 4.4418015E-03 0.7411346 at 30iterations 2.1025159E-03 0.3466568 at 40iterations 1.0086651E-03 0.1617661 at 50iterations finished qdiffx linear iterations at : 19:31:20 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 1.0086651E-03 0.1617661 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 19:31:20 3.601u 0.165s 0:04.06 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 Sun Oct 9 2011 at 19:31:20 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5531 !!! WARNING: ASL 282 has a net charge of -0.1000 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.508453 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): 3.140000 68.16600 ymin,ymax (A): -9.029000 53.44300 zmin,zma (A): -2.056000 68.74500 x,y,z range (A): 65.02600 62.47200 70.80099 scale (grids/A): 1.508453 object centre (A): 35.65300 22.20700 33.34450 number of atom coordinates read : 5531 total number of charged atoms : 5353 net assigned charge : 4.668028 assigned positive charge : 849.5988 centred at (gu) : 85.35279 88.01003 86.74903 assigned negative charge : -844.9370 centred at (gu) : 85.16960 88.11121 86.55515 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 102510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43658 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 31295 mr = 73974 m= 2694 mr = 21567 m= 47 mr = 1137 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 39868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 616 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 40029 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) : 0.5028178 object centre at (A) : 35.65300 22.20700 33.34450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3003609E-02 1.5590114E-02 midg,1,midg; midg,igrid,midg 1.1910375E-02 4.5263050E-03 1,midg,midg; igrid,midg,midg -9.1808764E-03 1.5735104E-03 gauss-seidel spectral radius is 0.9981011 estimated iterations to convergence 182 setup time was (sec) 0.7200000 now iterating at: 19:31:21 rms-change max change #iterations 4.088323 171.2483 at 10iterations 1.674452 52.56821 at 20iterations 0.6845239 23.25417 at 30iterations 0.2810639 8.488037 at 40iterations 0.1166499 3.784554 at 50iterations 4.9399085E-02 1.453522 at 60iterations 2.2271521E-02 0.7632370 at 70iterations 1.1420782E-02 0.3850460 at 80iterations 7.0374827E-03 0.2507706 at 90iterations 4.8679579E-03 0.1716003 at 100iterations 3.5751401E-03 0.1190643 at 110iterations 2.6793161E-03 8.6154938E-02 at 120iterations finished qdiffx linear iterations at : 19:31:28 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 2.6793161E-03 8.6154938E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 19:31:29 8.064u 0.203s 0:08.53 96.8% 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 Sun Oct 9 2011 at 19:31:29 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5531 !!! WARNING: ASL 282 has a net charge of -0.1000 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.262680 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): 3.140000 68.16600 ymin,ymax (A): -9.029000 53.44300 zmin,zma (A): -2.056000 68.74500 x,y,z range (A): 65.02600 62.47200 70.80099 scale (grids/A): 2.262680 object centre (A): 35.65300 22.20700 33.34450 number of atom coordinates read : 5531 total number of charged atoms : 5353 net assigned charge : 4.668028 assigned positive charge : 849.5988 centred at (gu) : 83.02892 87.01460 85.12305 assigned negative charge : -844.9370 centred at (gu) : 82.75445 87.16682 84.83282 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 238934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43658 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 112254 mr = 180735 m= 28842 mr = 89655 m= 3777 mr = 21283 m= 196 mr = 2295 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 89965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 42659 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) : 1.508453 object centre at (A) : 35.65300 22.20700 33.34450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3371711 0.5984570 midg,1,midg; midg,igrid,midg 0.2141590 4.2267799E-02 1,midg,midg; igrid,midg,midg -0.2558635 -1.6623276E-03 gauss-seidel spectral radius is 0.9991602 estimated iterations to convergence 273 setup time was (sec) 1.460000 now iterating at: 19:31:31 rms-change max change #iterations 10.94508 280.6302 at 10iterations 6.240190 147.0350 at 20iterations 3.523317 73.76181 at 30iterations 1.984376 38.29837 at 40iterations 1.113526 22.73428 at 50iterations 0.6219673 12.06589 at 60iterations 0.3472936 6.898708 at 70iterations 0.1940288 3.215961 at 80iterations 0.1084714 2.114166 at 90iterations 6.0779996E-02 1.172447 at 100iterations 3.4403604E-02 0.6353302 at 110iterations 1.9811116E-02 0.3621969 at 120iterations 1.1840522E-02 0.2441864 at 130iterations 7.5117974E-03 0.1525683 at 140iterations 5.1239720E-03 0.1056824 at 150iterations 3.7739696E-03 7.8353882E-02 at 160iterations 2.9377502E-03 5.7762146E-02 at 170iterations 2.3615265E-03 4.4601440E-02 at 180iterations finished qdiffx linear iterations at : 19:31:42 total time elapsed so far: 13.11000 # loops : 180 mean,max change (kT/e) : 2.3615265E-03 4.4601440E-02 energy calculations done at 13.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.24000 DelPhi exited at 19:31:43 13.245u 0.230s 0:13.77 97.8% 0+0k 0+0io 0pf+0w