Mon Oct 10 23:52:02 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+sph.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 = amb.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 23:52:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2597 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: 0.6166958 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): 10.25900 64.58200 ymin,ymax (A): -1.347000 56.38000 zmin,zma (A): 10.20500 53.85700 x,y,z range (A): 54.32300 57.72700 43.65200 scale (grids/A): 0.6166958 object centre (A): 37.42050 27.51650 32.03100 number of atom coordinates read : 2597 total number of charged atoms : 2457 net assigned charge : 9.000027 assigned positive charge : 389.4888 centred at (gu) : 88.74033 91.56443 89.48472 assigned negative charge : -380.4895 centred at (gu) : 88.73089 91.38686 89.63944 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6496 nv = 96 ne = 84 npr = 52685 no. pairs analyzed = 52685 no. exposed pairs = 3105 no. arc points = 21675 no. surface atoms = 1054 nbur = 1543 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 338 mr = 3638 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3200000 number of dielectric boundary points 3156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2172 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8094 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7113162E-08 -2.6154250E-09 midg,1,midg; midg,igrid,midg -2.9972826E-09 2.3483473E-08 1,midg,midg; igrid,midg,midg 7.5255340E-09 5.2477169E-09 gauss-seidel spectral radius is 0.9863805 estimated iterations to convergence 70 setup time was (sec) 0.5600000 now iterating at: 23:52:03 rms-change max change #iterations 0.1215786 19.56006 at 10iterations 1.2258755E-02 1.934990 at 20iterations 1.6948051E-03 0.3519592 at 30iterations 4.2590237E-04 0.1008339 at 40iterations 1.2564563E-04 3.0235291E-02 at 50iterations finished qdiffx linear iterations at : 23:52:05 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.2564563E-04 3.0235291E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 23:52:06 3.385u 0.140s 0:04.20 83.8% 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 Mon Oct 10 2011 at 23:52:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2597 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: 1.850087 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): 10.25900 64.58200 ymin,ymax (A): -1.347000 56.38000 zmin,zma (A): 10.20500 53.85700 x,y,z range (A): 54.32300 57.72700 43.65200 scale (grids/A): 1.850087 object centre (A): 37.42050 27.51650 32.03100 number of atom coordinates read : 2597 total number of charged atoms : 2457 net assigned charge : 9.000027 assigned positive charge : 389.4888 centred at (gu) : 86.22021 94.69266 88.45344 assigned negative charge : -380.4895 centred at (gu) : 86.19231 94.16039 88.91799 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 70630 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21675 grid for indexing accessible points = 1.400000 m= 24840 mr = 49413 m= 3597 mr = 18289 m= 141 mr = 2225 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1098 time to turn everything in is 0.5700000 number of dielectric boundary points 29252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19271 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) : 0.6166958 object centre at (A) : 37.42050 27.51650 32.03100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5218272E-02 4.1164788E-03 midg,1,midg; midg,igrid,midg -1.3244811E-02 2.1975737E-02 1,midg,midg; igrid,midg,midg -1.1128848E-03 1.7302638E-02 gauss-seidel spectral radius is 0.9985495 estimated iterations to convergence 208 setup time was (sec) 0.8900000 now iterating at: 23:52:07 rms-change max change #iterations 3.969627 166.2201 at 10iterations 1.809028 64.86047 at 20iterations 0.8256676 29.13171 at 30iterations 0.3784280 12.25558 at 40iterations 0.1736675 5.688441 at 50iterations 7.9694524E-02 2.645252 at 60iterations 3.6642510E-02 1.187579 at 70iterations 1.6886655E-02 0.5375710 at 80iterations 7.9545761E-03 0.2669387 at 90iterations 3.7935644E-03 0.1372261 at 100iterations 1.8951885E-03 7.1437836E-02 at 110iterations 1.0102298E-03 4.1984558E-02 at 120iterations finished qdiffx linear iterations at : 23:52:14 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 1.0102298E-03 4.1984558E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 23:52:15 8.205u 0.210s 0:08.99 93.5% 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 Mon Oct 10 2011 at 23:52:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2597 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: 2.775131 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): 10.25900 64.58200 ymin,ymax (A): -1.347000 56.38000 zmin,zma (A): 10.20500 53.85700 x,y,z range (A): 54.32300 57.72700 43.65200 scale (grids/A): 2.775131 object centre (A): 37.42050 27.51650 32.03100 number of atom coordinates read : 2597 total number of charged atoms : 2457 net assigned charge : 9.000027 assigned positive charge : 389.4888 centred at (gu) : 84.33005 97.03879 87.68004 assigned negative charge : -380.4895 centred at (gu) : 84.28833 96.24050 88.37688 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 163406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21675 grid for indexing accessible points = 1.400000 m= 81428 mr = 119783 m= 28566 mr = 66648 m= 6433 mr = 23039 m= 770 mr = 4843 m= 27 mr = 456 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 3600 time to turn everything in is 1.360000 number of dielectric boundary points 65858 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 19653 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) : 1.850087 object centre at (A) : 37.42050 27.51650 32.03100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4029706 6.7491554E-02 midg,1,midg; midg,igrid,midg -0.3582931 -0.2056612 1,midg,midg; igrid,midg,midg -9.4214603E-02 0.1039135 gauss-seidel spectral radius is 0.9992293 estimated iterations to convergence 284 setup time was (sec) 1.700000 now iterating at: 23:52:17 rms-change max change #iterations 9.385950 405.6475 at 10iterations 5.393115 142.0494 at 20iterations 3.075812 79.80264 at 30iterations 1.750312 37.59167 at 40iterations 0.9947968 18.76044 at 50iterations 0.5673234 12.93093 at 60iterations 0.3229253 6.484793 at 70iterations 0.1836921 3.315542 at 80iterations 0.1043463 1.873135 at 90iterations 5.9362948E-02 1.071014 at 100iterations 3.3747520E-02 0.6130981 at 110iterations 1.9282995E-02 0.4634628 at 120iterations 1.1086598E-02 0.2202263 at 130iterations 6.4182524E-03 0.1268158 at 140iterations 3.7776821E-03 7.7415466E-02 at 150iterations 2.2929295E-03 4.8549652E-02 at 160iterations 1.4566735E-03 3.4309387E-02 at 170iterations 9.7719219E-04 2.6142120E-02 at 180iterations finished qdiffx linear iterations at : 23:52:28 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 9.7719219E-04 2.6142120E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 23:52:29 12.730u 0.238s 0:13.48 96.1% 0+0k 0+0io 0pf+0w