Mon Oct 10 09:44:43 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 Mon Oct 10 2011 at 09:44:43 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2842 !!! WARNING: HIT 235 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5649986 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): 112.5730 175.5820 ymin,ymax (A): -42.56600 10.38600 zmin,zma (A): 46.55200 102.4840 x,y,z range (A): 63.00900 52.95200 55.93200 scale (grids/A): 0.5649986 object centre (A): 144.0775 -16.09000 74.51801 number of atom coordinates read : 2842 total number of charged atoms : 2692 net assigned charge : 7.014015 assigned positive charge : 417.3998 centred at (gu) : 89.45187 88.91432 89.49444 assigned negative charge : -410.3864 centred at (gu) : 89.53834 89.03682 89.31077 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5977 nv = 96 ne = 84 npr = 55730 no. pairs analyzed = 55730 no. exposed pairs = 4274 no. arc points = 31210 no. surface atoms = 1408 nbur = 1434 mkacc time = 0.1200000 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 = 1.512000 m= 314 mr = 2583 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3701 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3016 ## 380 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7660 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5922970E-09 2.7250120E-09 midg,1,midg; midg,igrid,midg 3.0641263E-09 -4.7313664E-10 1,midg,midg; igrid,midg,midg 2.2009223E-09 -1.4977496E-10 gauss-seidel spectral radius is 0.9838421 estimated iterations to convergence 65 setup time was (sec) 0.5100000 now iterating at: 09:44:43 rms-change max change #iterations 8.3611622E-02 14.34340 at 10iterations 5.9544230E-03 1.031677 at 20iterations 4.2157096E-04 6.5290451E-02 at 30iterations 3.5424418E-05 5.5055618E-03 at 40iterations 4.1440467E-06 6.4659119E-04 at 50iterations finished qdiffx linear iterations at : 09:44:46 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 4.1440467E-06 6.4659119E-04 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 09:44:46 3.235u 0.165s 0:03.67 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 09:44:46 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2842 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.694996 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): 112.5730 175.5820 ymin,ymax (A): -42.56600 10.38600 zmin,zma (A): 46.55200 102.4840 x,y,z range (A): 63.00900 52.95200 55.93200 scale (grids/A): 1.694996 object centre (A): 144.0775 -16.09000 74.51801 number of atom coordinates read : 2842 total number of charged atoms : 2692 net assigned charge : 7.014015 assigned positive charge : 417.3998 centred at (gu) : 88.35515 86.74236 88.48283 assigned negative charge : -410.3864 centred at (gu) : 88.61453 87.11035 87.93198 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 63627 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31210 grid for indexing accessible points = 1.400000 m= 20161 mr = 38331 m= 2546 mr = 12595 m= 100 mr = 1138 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 34360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 20792 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) : 0.5649986 object centre at (A) : 144.0775 -16.09000 74.51801 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1639744E-02 2.0660514E-02 midg,1,midg; midg,igrid,midg 1.8150060E-02 3.8916417E-03 1,midg,midg; igrid,midg,midg 1.3919579E-02 7.1598585E-03 gauss-seidel spectral radius is 0.9983296 estimated iterations to convergence 194 setup time was (sec) 0.7400000 now iterating at: 09:44:47 rms-change max change #iterations 3.435944 186.5610 at 10iterations 1.475852 60.04457 at 20iterations 0.6347061 24.92065 at 30iterations 0.2743572 10.28892 at 40iterations 0.1177066 4.755239 at 50iterations 5.0740752E-02 1.793991 at 60iterations 2.1846162E-02 0.8031769 at 70iterations 9.4231665E-03 0.3696098 at 80iterations 4.0476983E-03 0.1433938 at 90iterations 1.7501756E-03 6.8080902E-02 at 100iterations 7.5573818E-04 2.7379990E-02 at 110iterations 3.2512072E-04 1.3061523E-02 at 120iterations finished qdiffx linear iterations at : 09:44:53 total time elapsed so far: 6.680000 # loops : 120 mean,max change (kT/e) : 3.2512072E-04 1.3061523E-02 energy calculations done at 6.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.860000 DelPhi exited at 09:44:54 6.859u 0.160s 0:07.29 96.1% 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 09:44:54 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2842 !!! WARNING: HIT 235 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.542494 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): 112.5730 175.5820 ymin,ymax (A): -42.56600 10.38600 zmin,zma (A): 46.55200 102.4840 x,y,z range (A): 63.00900 52.95200 55.93200 scale (grids/A): 2.542494 object centre (A): 144.0775 -16.09000 74.51801 number of atom coordinates read : 2842 total number of charged atoms : 2692 net assigned charge : 7.014015 assigned positive charge : 417.3998 centred at (gu) : 87.53252 85.11340 87.72411 assigned negative charge : -410.3864 centred at (gu) : 87.92171 85.66550 86.89790 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 146946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31210 grid for indexing accessible points = 1.400000 m= 65532 mr = 94680 m= 21213 mr = 48412 m= 4020 mr = 14971 m= 333 mr = 2334 m= 20 mr = 137 m= 0 mr = 6 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 77524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 21530 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) : 1.694996 object centre at (A) : 144.0775 -16.09000 74.51801 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1367274 0.2721417 midg,1,midg; midg,igrid,midg 0.2590312 8.2859799E-02 1,midg,midg; igrid,midg,midg 0.2227988 6.6914827E-02 gauss-seidel spectral radius is 0.9991987 estimated iterations to convergence 279 setup time was (sec) 1.370000 now iterating at: 09:44:55 rms-change max change #iterations 8.968030 331.0005 at 10iterations 5.248016 174.7745 at 20iterations 3.028094 76.34970 at 30iterations 1.734107 42.29925 at 40iterations 0.9854976 22.21174 at 50iterations 0.5611309 13.67338 at 60iterations 0.3170103 8.777742 at 70iterations 0.1791530 3.992100 at 80iterations 0.1011930 2.202215 at 90iterations 5.7023492E-02 1.279267 at 100iterations 3.2095298E-02 0.6866427 at 110iterations 1.8069111E-02 0.3577560 at 120iterations 1.0137849E-02 0.2168522 at 130iterations 5.6885649E-03 0.1165895 at 140iterations 3.2014782E-03 7.4361324E-02 at 150iterations 1.7941428E-03 3.9930344E-02 at 160iterations 1.0081121E-03 2.1575928E-02 at 170iterations 5.6536339E-04 1.2359619E-02 at 180iterations finished qdiffx linear iterations at : 09:45:05 total time elapsed so far: 10.81000 # loops : 180 mean,max change (kT/e) : 5.6536339E-04 1.2359619E-02 energy calculations done at 10.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.99000 DelPhi exited at 09:45:05 10.988u 0.178s 0:11.59 96.2% 0+0k 0+0io 0pf+0w