Sun Oct 9 14:09:00 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 14:09:00 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2432 !!! WARNING: SEP 248 has a net charge of -0.4750 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: 0.6708374 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): -8.543000 37.18500 ymin,ymax (A): 1.464000 52.27700 zmin,zma (A): -5.235000 47.83300 x,y,z range (A): 45.72800 50.81300 53.06800 scale (grids/A): 0.6708374 object centre (A): 14.32100 26.87050 21.29900 number of atom coordinates read : 2432 total number of charged atoms : 2307 net assigned charge : 5.025017 assigned positive charge : 366.0679 centred at (gu) : 88.72751 90.92712 89.71256 assigned negative charge : -361.0437 centred at (gu) : 88.82170 91.00599 89.78074 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7548 nv = 96 ne = 84 npr = 48376 no. pairs analyzed = 48376 no. exposed pairs = 3181 no. arc points = 22198 no. surface atoms = 1057 nbur = 1375 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 451 mr = 4089 m= 2 mr = 26 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 0.3000000 number of dielectric boundary points 3886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2089 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8644 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5188794E-08 3.1683353E-10 midg,1,midg; midg,igrid,midg 2.9614897E-08 -3.0805010E-09 1,midg,midg; igrid,midg,midg 5.1146777E-08 -4.4912962E-09 gauss-seidel spectral radius is 0.9884706 estimated iterations to convergence 76 setup time was (sec) 0.5100000 now iterating at: 14:09:00 rms-change max change #iterations 0.1737071 31.61317 at 10iterations 1.8654021E-02 2.588470 at 20iterations 2.1167276E-03 0.2564468 at 30iterations 2.4677152E-04 3.3758163E-02 at 40iterations 3.3681499E-05 4.4155121E-03 at 50iterations finished qdiffx linear iterations at : 14:09:03 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 3.3681499E-05 4.4155121E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 14:09:03 3.116u 0.143s 0:03.54 91.8% 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 Sun Oct 9 2011 at 14:09:03 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2432 !!! WARNING: SEP 248 has a net charge of -0.4750 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: 2.012512 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): -8.543000 37.18500 ymin,ymax (A): 1.464000 52.27700 zmin,zma (A): -5.235000 47.83300 x,y,z range (A): 45.72800 50.81300 53.06800 scale (grids/A): 2.012512 object centre (A): 14.32100 26.87050 21.29900 number of atom coordinates read : 2432 total number of charged atoms : 2307 net assigned charge : 5.025017 assigned positive charge : 366.0679 centred at (gu) : 86.18215 92.78082 89.13712 assigned negative charge : -361.0437 centred at (gu) : 86.46484 93.01794 89.34212 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 80306 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22198 grid for indexing accessible points = 1.400000 m= 30434 mr = 55088 m= 5138 mr = 22085 m= 342 mr = 3126 m= 7 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 35797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 18250 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) : 0.6708374 object centre at (A) : 14.32100 26.87050 21.29900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6711951E-02 1.2927368E-02 midg,1,midg; midg,igrid,midg 5.7924490E-02 2.7675025E-02 1,midg,midg; igrid,midg,midg 5.2984077E-03 -4.0776182E-02 gauss-seidel spectral radius is 0.9987656 estimated iterations to convergence 225 setup time was (sec) 0.8100000 now iterating at: 14:09:04 rms-change max change #iterations 4.512968 219.9918 at 10iterations 2.190947 75.66561 at 20iterations 1.062011 36.07446 at 30iterations 0.5171482 15.73257 at 40iterations 0.2513375 8.023880 at 50iterations 0.1217561 3.644432 at 60iterations 5.9179686E-02 1.788893 at 70iterations 2.8865058E-02 0.8571117 at 80iterations 1.3994138E-02 0.4399261 at 90iterations 6.7951716E-03 0.2155781 at 100iterations 3.3006889E-03 0.1110477 at 110iterations 1.6056835E-03 5.3974152E-02 at 120iterations finished qdiffx linear iterations at : 14:09:10 total time elapsed so far: 6.730000 # loops : 120 mean,max change (kT/e) : 1.6056835E-03 5.3974152E-02 energy calculations done at 6.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.910000 DelPhi exited at 14:09:11 6.910u 0.166s 0:07.35 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 Sun Oct 9 2011 at 14:09:11 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2432 !!! WARNING: SEP 248 has a net charge of -0.4750 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: 3.018768 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): -8.543000 37.18500 ymin,ymax (A): 1.464000 52.27700 zmin,zma (A): -5.235000 47.83300 x,y,z range (A): 45.72800 50.81300 53.06800 scale (grids/A): 3.018768 object centre (A): 14.32100 26.87050 21.29900 number of atom coordinates read : 2432 total number of charged atoms : 2307 net assigned charge : 5.025017 assigned positive charge : 366.0679 centred at (gu) : 84.27311 94.17113 88.70556 assigned negative charge : -361.0437 centred at (gu) : 84.69721 94.52679 89.01308 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 184998 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22198 grid for indexing accessible points = 1.400000 m= 96194 mr = 133407 m= 36778 mr = 77871 m= 9344 mr = 29213 m= 1450 mr = 6843 m= 138 mr = 929 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.450000 number of dielectric boundary points 80576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 18451 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) : 2.012512 object centre at (A) : 14.32100 26.87050 21.29900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9412864 3.1007430E-02 midg,1,midg; midg,igrid,midg 0.6956779 0.1944314 1,midg,midg; igrid,midg,midg 2.7303571E-02 -0.3823532 gauss-seidel spectral radius is 0.9992930 estimated iterations to convergence 297 setup time was (sec) 1.760000 now iterating at: 14:09:12 rms-change max change #iterations 10.55745 444.2198 at 10iterations 6.325697 134.4951 at 20iterations 3.761056 79.63988 at 30iterations 2.227369 50.50422 at 40iterations 1.316216 25.84093 at 50iterations 0.7746527 14.39196 at 60iterations 0.4555743 7.795300 at 70iterations 0.2670609 4.776379 at 80iterations 0.1564787 2.541735 at 90iterations 9.1555499E-02 1.462610 at 100iterations 5.3517796E-02 0.9291035 at 110iterations 3.1264957E-02 0.5571690 at 120iterations 1.8285675E-02 0.3760147 at 130iterations 1.0688091E-02 0.1871128 at 140iterations 6.2460196E-03 0.1171112 at 150iterations 3.6570074E-03 6.0836792E-02 at 160iterations 2.1574886E-03 3.9652824E-02 at 170iterations 1.2760066E-03 2.4099350E-02 at 180iterations finished qdiffx linear iterations at : 14:09:22 total time elapsed so far: 11.50000 # loops : 180 mean,max change (kT/e) : 1.2760066E-03 2.4099350E-02 energy calculations done at 11.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.71000 DelPhi exited at 14:09:23 11.712u 0.169s 0:12.22 97.1% 0+0k 0+0io 0pf+0w