Sun Oct 9 19:24:41 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 19:24:41 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5113 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5482575 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): 3.236000 68.16900 ymin,ymax (A): -8.569000 53.47100 zmin,zma (A): -1.199000 62.04500 x,y,z range (A): 64.93300 62.04000 63.24400 scale (grids/A): 0.5482575 object centre (A): 35.70250 22.45100 30.42300 number of atom coordinates read : 5113 total number of charged atoms : 4965 net assigned charge : 0.6350474 assigned positive charge : 786.3657 centred at (gu) : 87.86415 89.13159 89.27487 assigned negative charge : -785.7368 centred at (gu) : 87.72795 89.17913 89.24995 start vw surface at 0.2500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 10033 nv = 96 ne = 84 npr = 103757 no. pairs analyzed = 103757 no. exposed pairs = 6049 no. arc points = 40898 no. surface atoms = 2061 nbur = 3052 mkacc time = 0.2600000 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 = 1.568000 m= 412 mr = 5696 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2899999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 4727 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4126 ## 476 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 13169 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8249533E-10 3.3185793E-10 midg,1,midg; midg,igrid,midg 8.4789631E-10 -4.2185386E-10 1,midg,midg; igrid,midg,midg -2.8865219E-09 1.0502794E-09 gauss-seidel spectral radius is 0.9829988 estimated iterations to convergence 63 setup time was (sec) 0.8800000 now iterating at: 19:24:42 rms-change max change #iterations 0.1042694 15.07479 at 10iterations 9.3311518E-03 1.222031 at 20iterations 2.7992120E-03 0.3197861 at 30iterations 1.3350805E-03 0.1446660 at 40iterations 6.5919326E-04 7.6420784E-02 at 50iterations finished qdiffx linear iterations at : 19:24:46 total time elapsed so far: 4.450000 # loops : 50 mean,max change (kT/e) : 6.5919326E-04 7.6420784E-02 energy calculations done at 4.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 19:24:46 4.637u 0.277s 0:05.18 94.5% 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 Sun Oct 9 2011 at 19:24:46 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5113 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.644772 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): 3.236000 68.16900 ymin,ymax (A): -8.569000 53.47100 zmin,zma (A): -1.199000 62.04500 x,y,z range (A): 64.93300 62.04000 63.24400 scale (grids/A): 1.644772 object centre (A): 35.70250 22.45100 30.42300 number of atom coordinates read : 5113 total number of charged atoms : 4965 net assigned charge : 0.6350474 assigned positive charge : 786.3657 centred at (gu) : 83.59100 87.39314 87.82321 assigned negative charge : -785.7368 centred at (gu) : 83.18384 87.53731 87.75000 start vw surface at 0.1900000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 112086 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40898 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 38388 mr = 81140 m= 4502 mr = 27667 m= 124 mr = 2368 m= 0 mr = 6 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 43919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 382 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 38094 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) : 0.5482575 object centre at (A) : 35.70250 22.45100 30.42300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3159636E-02 -1.7535724E-02 midg,1,midg; midg,igrid,midg 1.7917514E-02 7.5314911E-03 1,midg,midg; igrid,midg,midg -2.4072334E-02 2.3965808E-02 gauss-seidel spectral radius is 0.9984057 estimated iterations to convergence 199 setup time was (sec) 1.170000 now iterating at: 19:24:48 rms-change max change #iterations 4.741023 178.5348 at 10iterations 2.089872 60.51300 at 20iterations 0.9221146 26.88486 at 30iterations 0.4066041 11.95376 at 40iterations 0.1803210 5.224567 at 50iterations 7.9676174E-02 2.204406 at 60iterations 3.5826862E-02 1.006262 at 70iterations 1.6368534E-02 0.4826813 at 80iterations 8.0166655E-03 0.2719193 at 90iterations 4.4157440E-03 0.1123123 at 100iterations 2.8053890E-03 7.5714111E-02 at 110iterations 1.9995598E-03 4.8698425E-02 at 120iterations finished qdiffx linear iterations at : 19:24:57 total time elapsed so far: 10.23000 # loops : 120 mean,max change (kT/e) : 1.9995598E-03 4.8698425E-02 energy calculations done at 10.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.42000 DelPhi exited at 19:24:57 10.421u 0.336s 0:11.05 97.2% 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 Sun Oct 9 2011 at 19:24:58 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5113 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.467159 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): 3.236000 68.16900 ymin,ymax (A): -8.569000 53.47100 zmin,zma (A): -1.199000 62.04500 x,y,z range (A): 64.93300 62.04000 63.24400 scale (grids/A): 2.467159 object centre (A): 35.70250 22.45100 30.42300 number of atom coordinates read : 5113 total number of charged atoms : 4965 net assigned charge : 0.6350474 assigned positive charge : 786.3657 centred at (gu) : 80.38627 86.08926 86.73448 assigned negative charge : -785.7368 centred at (gu) : 79.77587 86.30605 86.62505 start vw surface at 0.2000000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 260781 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40898 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 130861 mr = 197882 m= 40757 mr = 106539 m= 7073 mr = 31383 m= 544 mr = 4790 m= 4 mr = 241 m= 0 mr = 0 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.120000 number of dielectric boundary points 99185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 39683 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) : 1.644772 object centre at (A) : 35.70250 22.45100 30.42300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3584983 -0.3957538 midg,1,midg; midg,igrid,midg 9.5567845E-02 -6.7245918E-03 1,midg,midg; igrid,midg,midg -0.4833252 0.3635489 gauss-seidel spectral radius is 0.9992476 estimated iterations to convergence 288 setup time was (sec) 2.510000 now iterating at: 19:25:00 rms-change max change #iterations 12.07613 320.6276 at 10iterations 7.111178 138.8992 at 20iterations 4.143399 84.20046 at 30iterations 2.415427 51.45889 at 40iterations 1.398778 25.46852 at 50iterations 0.8103058 14.65905 at 60iterations 0.4675499 7.803503 at 70iterations 0.2690704 4.236669 at 80iterations 0.1553013 2.475821 at 90iterations 8.9415215E-02 1.389717 at 100iterations 5.1594451E-02 0.8267460 at 110iterations 2.9828668E-02 0.5041599 at 120iterations 1.7428890E-02 0.2975922 at 130iterations 1.0382981E-02 0.1805496 at 140iterations 6.4278208E-03 0.1117296 at 150iterations 4.2006513E-03 7.8051567E-02 at 160iterations 2.9546879E-03 5.0666809E-02 at 170iterations 2.2356182E-03 3.5028458E-02 at 180iterations finished qdiffx linear iterations at : 19:25:15 total time elapsed so far: 17.66000 # loops : 180 mean,max change (kT/e) : 2.2356182E-03 3.5028458E-02 energy calculations done at 17.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.85000 DelPhi exited at 19:25:16 17.849u 0.346s 0:18.47 98.4% 0+0k 0+0io 0pf+0w