Sun Oct 9 19:30:55 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 Sun Oct 9 2011 at 19:30:55 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: 339 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5392 !!! WARNING: GLU 162 has a net charge of -0.5000 !!! 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5129831 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): 3.171000 68.16300 ymin,ymax (A): -9.049000 53.34000 zmin,zma (A): -2.113000 67.28500 x,y,z range (A): 64.99200 62.38900 69.39800 scale (grids/A): 0.5129831 object centre (A): 35.66700 22.14550 32.58600 number of atom coordinates read : 5392 total number of charged atoms : 5214 net assigned charge : 5.254027 assigned positive charge : 830.3283 centred at (gu) : 88.23965 89.32446 88.94890 assigned negative charge : -825.0801 centred at (gu) : 88.16054 89.33642 88.85004 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9069 nv = 96 ne = 84 npr = 109949 no. pairs analyzed = 109949 no. exposed pairs = 6193 no. arc points = 42293 no. surface atoms = 2109 nbur = 3283 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 = 1.680000 m= 328 mr = 5116 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4209 ## 579 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 12102 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1792644E-10 3.1334424E-10 midg,1,midg; midg,igrid,midg 1.5580615E-10 4.3891727E-11 1,midg,midg; igrid,midg,midg -2.7941119E-10 2.2067838E-10 gauss-seidel spectral radius is 0.9806018 estimated iterations to convergence 59 setup time was (sec) 0.7700000 now iterating at: 19:30:56 rms-change max change #iterations 8.2858808E-02 11.88433 at 10iterations 1.0118655E-02 1.550640 at 20iterations 4.0495037E-03 0.6929741 at 30iterations 1.8524070E-03 0.3153076 at 40iterations 8.5764495E-04 0.1430588 at 50iterations finished qdiffx linear iterations at : 19:30:59 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 8.5764495E-04 0.1430588 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 19:30:59 3.630u 0.150s 0:04.13 91.5% 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 19:30:59 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: 339 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5392 !!! WARNING: GLU 162 has a net charge of -0.5000 !!! 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.538949 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): 3.171000 68.16300 ymin,ymax (A): -9.049000 53.34000 zmin,zma (A): -2.113000 67.28500 x,y,z range (A): 64.99200 62.38900 69.39800 scale (grids/A): 1.538949 object centre (A): 35.66700 22.14550 32.58600 number of atom coordinates read : 5392 total number of charged atoms : 5214 net assigned charge : 5.254027 assigned positive charge : 830.3283 centred at (gu) : 84.71759 87.97189 86.84529 assigned negative charge : -825.0801 centred at (gu) : 84.48127 88.00933 86.55036 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 103604 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42293 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 32211 mr = 74873 m= 2980 mr = 22400 m= 61 mr = 1369 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 40208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 581 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 39174 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) : 0.5129831 object centre at (A) : 35.66700 22.14550 32.58600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3615231E-02 2.9844027E-02 midg,1,midg; midg,igrid,midg 1.3534775E-02 6.5226313E-03 1,midg,midg; igrid,midg,midg -1.3358609E-02 -3.1628564E-04 gauss-seidel spectral radius is 0.9981737 estimated iterations to convergence 186 setup time was (sec) 1.040000 now iterating at: 19:31:00 rms-change max change #iterations 4.198509 148.5095 at 10iterations 1.745510 60.74861 at 20iterations 0.7290000 23.20247 at 30iterations 0.3043417 8.796503 at 40iterations 0.1275265 3.839639 at 50iterations 5.4855049E-02 1.715162 at 60iterations 2.4834771E-02 0.8567505 at 70iterations 1.2634262E-02 0.4190521 at 80iterations 7.5947521E-03 0.2608261 at 90iterations 5.1811314E-03 0.1711655 at 100iterations 3.7847240E-03 0.1198273 at 110iterations 2.8276981E-03 8.9378357E-02 at 120iterations finished qdiffx linear iterations at : 19:31:07 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 2.8276981E-03 8.9378357E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 19:31:08 7.852u 0.203s 0:08.32 96.7% 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 19:31:08 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: 339 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5392 !!! WARNING: GLU 162 has a net charge of -0.5000 !!! 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.308424 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): 3.171000 68.16300 ymin,ymax (A): -9.049000 53.34000 zmin,zma (A): -2.113000 67.28500 x,y,z range (A): 64.99200 62.38900 69.39800 scale (grids/A): 2.308424 object centre (A): 35.66700 22.14550 32.58600 number of atom coordinates read : 5392 total number of charged atoms : 5214 net assigned charge : 5.254027 assigned positive charge : 830.3283 centred at (gu) : 82.07601 86.95767 85.26754 assigned negative charge : -825.0801 centred at (gu) : 81.72186 87.01404 84.82530 start vw surface at 0.2100000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 241725 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42293 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 114492 mr = 183139 m= 30829 mr = 92074 m= 4409 mr = 22999 m= 232 mr = 2694 m= 5 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.840000 number of dielectric boundary points 90698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 41588 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) : 1.538949 object centre at (A) : 35.66700 22.14550 32.58600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3446699 0.8680384 midg,1,midg; midg,igrid,midg 0.2080805 5.3317685E-02 1,midg,midg; igrid,midg,midg -0.3209123 -1.4394059E-02 gauss-seidel spectral radius is 0.9991812 estimated iterations to convergence 276 setup time was (sec) 2.160000 now iterating at: 19:31:10 rms-change max change #iterations 11.12812 269.3159 at 10iterations 6.386004 169.2649 at 20iterations 3.628577 75.53757 at 30iterations 2.057478 48.64586 at 40iterations 1.161065 21.64806 at 50iterations 0.6539125 12.31858 at 60iterations 0.3679549 6.401062 at 70iterations 0.2069775 3.527785 at 80iterations 0.1165939 2.167406 at 90iterations 6.5900840E-02 1.221832 at 100iterations 3.7559081E-02 0.6840229 at 110iterations 2.1819929E-02 0.3990326 at 120iterations 1.3185857E-02 0.2567768 at 130iterations 8.4575526E-03 0.1698341 at 140iterations 5.8224779E-03 0.1269836 at 150iterations 4.3145474E-03 8.4899902E-02 at 160iterations 3.3812393E-03 6.7626953E-02 at 170iterations 2.7321603E-03 5.0895691E-02 at 180iterations finished qdiffx linear iterations at : 19:31:20 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 2.7321603E-03 5.0895691E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 19:31:21 12.927u 0.215s 0:13.44 97.6% 0+0k 0+0io 0pf+0w