Sat Oct 8 11:38:49 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 Sat Oct 8 2011 at 11:38:49 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 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: 0.5947111 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): -27.20500 32.65600 ymin,ymax (A): -4.051000 43.94200 zmin,zma (A): -1.855000 52.63400 x,y,z range (A): 59.86100 47.99300 54.48900 scale (grids/A): 0.5947111 object centre (A): 2.725499 19.94550 25.38950 number of atom coordinates read : 2869 total number of charged atoms : 2718 net assigned charge : 0.5000079 assigned positive charge : 423.3383 centred at (gu) : 90.72973 89.32681 88.44215 assigned negative charge : -422.8391 centred at (gu) : 90.70580 89.33092 88.41346 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6890 nv = 96 ne = 84 npr = 56066 no. pairs analyzed = 56066 no. exposed pairs = 4028 no. arc points = 28876 no. surface atoms = 1330 nbur = 1539 mkacc time = 0.1500000 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 = 1.456000 m= 328 mr = 3341 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2856 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8539 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1277046E-09 8.0396390E-10 midg,1,midg; midg,igrid,midg 3.8070613E-10 4.4405930E-11 1,midg,midg; igrid,midg,midg -5.1974408E-10 1.1725750E-09 gauss-seidel spectral radius is 0.9854041 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 11:38:50 rms-change max change #iterations 0.1080983 17.05279 at 10iterations 8.9301346E-03 1.319662 at 20iterations 7.4751978E-04 0.1180992 at 30iterations 6.1577266E-05 9.6783638E-03 at 40iterations 5.2194714E-06 9.9563599E-04 at 50iterations finished qdiffx linear iterations at : 11:38:54 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 5.2194714E-06 9.9563599E-04 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 11:38:55 4.495u 0.413s 0:05.17 94.7% 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 Sat Oct 8 2011 at 11:38:55 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.784133 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): -27.20500 32.65600 ymin,ymax (A): -4.051000 43.94200 zmin,zma (A): -1.855000 52.63400 x,y,z range (A): 59.86100 47.99300 54.48900 scale (grids/A): 1.784133 object centre (A): 2.725499 19.94550 25.38950 number of atom coordinates read : 2869 total number of charged atoms : 2718 net assigned charge : 0.5000079 assigned positive charge : 423.3383 centred at (gu) : 92.18877 87.97958 85.32550 assigned negative charge : -422.8391 centred at (gu) : 92.11695 87.99223 85.23978 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28876 grid for indexing accessible points = 1.400000 m= 24523 mr = 48465 m= 3247 mr = 16536 m= 163 mr = 1715 m= 0 mr = 45 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 363 time to turn everything in is 0.6000000 number of dielectric boundary points 35664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 274 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 21185 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) : 0.5947111 object centre at (A) : 2.725499 19.94550 25.38950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0424626E-02 1.7093150E-03 midg,1,midg; midg,igrid,midg 1.2565779E-02 7.0345569E-03 1,midg,midg; igrid,midg,midg -2.4146582E-03 -1.3905880E-02 gauss-seidel spectral radius is 0.9984950 estimated iterations to convergence 204 setup time was (sec) 0.9500000 now iterating at: 11:38:56 rms-change max change #iterations 3.900414 161.2368 at 10iterations 1.762022 57.00969 at 20iterations 0.7887894 25.85745 at 30iterations 0.3543728 11.95319 at 40iterations 0.1596754 5.580649 at 50iterations 7.1674757E-02 2.516905 at 60iterations 3.2189157E-02 1.094172 at 70iterations 1.4562638E-02 0.5128174 at 80iterations 6.5320083E-03 0.2407017 at 90iterations 2.9494718E-03 0.1060786 at 100iterations 1.3324796E-03 4.3716431E-02 at 110iterations 6.0083863E-04 1.9422054E-02 at 120iterations finished qdiffx linear iterations at : 11:39:06 total time elapsed so far: 10.45000 # loops : 120 mean,max change (kT/e) : 6.0083863E-04 1.9422054E-02 energy calculations done at 10.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.61000 DelPhi exited at 11:39:06 10.617u 0.454s 0:11.38 97.1% 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 Sat Oct 8 2011 at 11:39:06 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 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: 2.676200 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): -27.20500 32.65600 ymin,ymax (A): -4.051000 43.94200 zmin,zma (A): -1.855000 52.63400 x,y,z range (A): 59.86100 47.99300 54.48900 scale (grids/A): 2.676200 object centre (A): 2.725499 19.94550 25.38950 number of atom coordinates read : 2869 total number of charged atoms : 2718 net assigned charge : 0.5000079 assigned positive charge : 423.3383 centred at (gu) : 93.28306 86.96916 82.98824 assigned negative charge : -422.8391 centred at (gu) : 93.17529 86.98819 82.85961 start vw surface at 0.1300000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 172119 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28876 grid for indexing accessible points = 1.400000 m= 81220 mr = 118498 m= 25998 mr = 63148 m= 5330 mr = 19272 m= 657 mr = 3672 m= 25 mr = 383 m= 0 mr = 6 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 1253 time to turn everything in is 1.570000 number of dielectric boundary points 80370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 21738 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) : 1.784133 object centre at (A) : 2.725499 19.94550 25.38950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1417330 -5.0466303E-02 midg,1,midg; midg,igrid,midg 0.1754206 6.9511734E-02 1,midg,midg; igrid,midg,midg 0.4259661 -0.1741520 gauss-seidel spectral radius is 0.9992426 estimated iterations to convergence 287 setup time was (sec) 1.910000 now iterating at: 11:39:08 rms-change max change #iterations 9.776333 305.8163 at 10iterations 5.822429 144.9881 at 20iterations 3.408268 76.98813 at 30iterations 1.984768 40.77462 at 40iterations 1.150456 26.83871 at 50iterations 0.6663778 13.55079 at 60iterations 0.3842837 7.571089 at 70iterations 0.2210466 4.574831 at 80iterations 0.1266760 2.433776 at 90iterations 7.2884664E-02 1.365425 at 100iterations 4.1717552E-02 0.8140473 at 110iterations 2.3867374E-02 0.4362301 at 120iterations 1.3632011E-02 0.2658930 at 130iterations 7.8026042E-03 0.1462196 at 140iterations 4.4645495E-03 8.4275246E-02 at 150iterations 2.5495153E-03 4.7627449E-02 at 160iterations 1.4537232E-03 2.6727796E-02 at 170iterations 8.3326624E-04 1.6529083E-02 at 180iterations finished qdiffx linear iterations at : 11:39:25 total time elapsed so far: 18.57000 # loops : 180 mean,max change (kT/e) : 8.3326624E-04 1.6529083E-02 energy calculations done at 18.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.74000 DelPhi exited at 11:39:26 18.745u 0.470s 0:19.54 98.3% 0+0k 0+0io 0pf+0w