Tue Oct 11 06:55:36 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 Tue Oct 11 2011 at 06:55:36 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5629972 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): -20.33000 42.90300 ymin,ymax (A): 19.17300 77.44200 zmin,zma (A): -70.43200 -20.29900 x,y,z range (A): 63.23300 58.26900 50.13300 scale (grids/A): 0.5629972 object centre (A): 11.28650 48.30750 -45.36550 number of atom coordinates read : 2999 total number of charged atoms : 2857 net assigned charge : -2.446993 assigned positive charge : 440.2234 centred at (gu) : 90.30312 89.63274 89.73698 assigned negative charge : -442.6711 centred at (gu) : 90.25629 89.78822 89.74837 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6293 nv = 96 ne = 84 npr = 61539 no. pairs analyzed = 61539 no. exposed pairs = 3840 no. arc points = 27143 no. surface atoms = 1295 nbur = 1704 mkacc time = 0.1800000 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 = 1.540000 m= 259 mr = 3256 m= 0 mr = 8 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2738 ## 322 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 8026 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6940156E-10 -4.1302967E-10 midg,1,midg; midg,igrid,midg 1.7232863E-09 -2.0534043E-09 1,midg,midg; igrid,midg,midg -8.1592860E-10 2.9431105E-10 gauss-seidel spectral radius is 0.9837306 estimated iterations to convergence 64 setup time was (sec) 0.7000000 now iterating at: 06:55:37 rms-change max change #iterations 8.2242332E-02 11.89822 at 10iterations 5.9355083E-03 0.9462166 at 20iterations 4.2978075E-04 6.8077087E-02 at 30iterations 3.1209649E-05 5.0106049E-03 at 40iterations 2.3363857E-06 3.7384033E-04 at 50iterations finished qdiffx linear iterations at : 06:55:40 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 2.3363857E-06 3.7384033E-04 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 06:55:40 4.085u 0.180s 0:04.57 93.2% 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 Tue Oct 11 2011 at 06:55:40 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.688991 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): -20.33000 42.90300 ymin,ymax (A): 19.17300 77.44200 zmin,zma (A): -70.43200 -20.29900 x,y,z range (A): 63.23300 58.26900 50.13300 scale (grids/A): 1.688991 object centre (A): 11.28650 48.30750 -45.36550 number of atom coordinates read : 2999 total number of charged atoms : 2857 net assigned charge : -2.446993 assigned positive charge : 440.2234 centred at (gu) : 90.90858 88.89763 89.21056 assigned negative charge : -442.6711 centred at (gu) : 90.76851 89.36432 89.24502 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 68399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27143 grid for indexing accessible points = 1.400000 m= 22451 mr = 45961 m= 2622 mr = 15747 m= 86 mr = 1341 m= 0 mr = 12 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 202 time to turn everything in is 0.6400000 number of dielectric boundary points 30497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 228 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 22106 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) : 0.5629972 object centre at (A) : 11.28650 48.30750 -45.36550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7508011E-03 8.9307884E-03 midg,1,midg; midg,igrid,midg -4.0082200E-03 -9.7397100E-03 1,midg,midg; igrid,midg,midg 1.1098055E-04 -9.3956868E-04 gauss-seidel spectral radius is 0.9983171 estimated iterations to convergence 194 setup time was (sec) 0.9800000 now iterating at: 06:55:42 rms-change max change #iterations 3.567216 146.7115 at 10iterations 1.528677 57.81813 at 20iterations 0.6569382 24.32463 at 30iterations 0.2828392 11.26707 at 40iterations 0.1215545 4.486929 at 50iterations 5.2459292E-02 1.892441 at 60iterations 2.2620700E-02 0.8224945 at 70iterations 9.7269118E-03 0.3623636 at 80iterations 4.1980837E-03 0.1523947 at 90iterations 1.8031175E-03 5.8551788E-02 at 100iterations 7.7586831E-04 2.9753685E-02 at 110iterations 3.3535552E-04 1.2392998E-02 at 120iterations finished qdiffx linear iterations at : 06:55:49 total time elapsed so far: 8.640000 # loops : 120 mean,max change (kT/e) : 3.3535552E-04 1.2392998E-02 energy calculations done at 8.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.860000 DelPhi exited at 06:55:50 8.867u 0.203s 0:09.43 96.0% 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 Tue Oct 11 2011 at 06:55:50 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.533487 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): -20.33000 42.90300 ymin,ymax (A): 19.17300 77.44200 zmin,zma (A): -70.43200 -20.29900 x,y,z range (A): 63.23300 58.26900 50.13300 scale (grids/A): 2.533487 object centre (A): 11.28650 48.30750 -45.36550 number of atom coordinates read : 2999 total number of charged atoms : 2857 net assigned charge : -2.446993 assigned positive charge : 440.2234 centred at (gu) : 91.36274 88.34628 88.81566 assigned negative charge : -442.6711 centred at (gu) : 91.15261 89.04629 88.86734 start vw surface at 0.2100000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 158525 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27143 grid for indexing accessible points = 1.400000 m= 75195 mr = 112405 m= 23888 mr = 59813 m= 4222 mr = 18216 m= 316 mr = 2791 m= 7 mr = 139 m= 0 mr = 2 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 802 time to turn everything in is 1.520000 number of dielectric boundary points 68787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 22840 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) : 1.688991 object centre at (A) : 11.28650 48.30750 -45.36550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1111463 0.1679083 midg,1,midg; midg,igrid,midg -0.1002938 -0.1249174 1,midg,midg; igrid,midg,midg -1.5356583E-02 -2.4494091E-02 gauss-seidel spectral radius is 0.9991803 estimated iterations to convergence 276 setup time was (sec) 1.870000 now iterating at: 06:55:52 rms-change max change #iterations 9.104784 291.6274 at 10iterations 5.203659 119.7585 at 20iterations 2.956763 75.74468 at 30iterations 1.668891 36.82276 at 40iterations 0.9413306 21.46418 at 50iterations 0.5290149 12.70963 at 60iterations 0.2966919 6.949034 at 70iterations 0.1660807 3.414732 at 80iterations 9.2759073E-02 1.960281 at 90iterations 5.1868431E-02 1.048679 at 100iterations 2.8914548E-02 0.6142218 at 110iterations 1.6171791E-02 0.3510275 at 120iterations 8.9944648E-03 0.1801696 at 130iterations 5.0363108E-03 9.9028587E-02 at 140iterations 2.8026851E-03 5.2762985E-02 at 150iterations 1.5600935E-03 2.9043198E-02 at 160iterations 8.6911075E-04 1.8720627E-02 at 170iterations 4.8500832E-04 9.6547604E-03 at 180iterations finished qdiffx linear iterations at : 06:56:04 total time elapsed so far: 13.83000 # loops : 180 mean,max change (kT/e) : 4.8500832E-04 9.6547604E-03 energy calculations done at 13.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.06000 DelPhi exited at 06:56:05 14.066u 0.216s 0:14.67 97.2% 0+0k 0+0io 0pf+0w