Tue Oct 11 01:44:44 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 Tue Oct 11 2011 at 01:44:44 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 = 2692 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: 0.5945423 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): 17.98400 77.86200 ymin,ymax (A): -11.27900 44.51800 zmin,zma (A): -7.658000 35.10900 x,y,z range (A): 59.87800 55.79700 42.76700 scale (grids/A): 0.5945423 object centre (A): 47.92300 16.61950 13.72550 number of atom coordinates read : 2692 total number of charged atoms : 2549 net assigned charge : 7.500022 assigned positive charge : 408.0256 centred at (gu) : 88.43512 89.77110 89.89002 assigned negative charge : -400.5264 centred at (gu) : 88.67326 89.92059 90.02068 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6227 nv = 96 ne = 84 npr = 54324 no. pairs analyzed = 54324 no. exposed pairs = 3210 no. arc points = 22740 no. surface atoms = 1085 nbur = 1607 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 303 mr = 3449 m= 0 mr = 31 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3100000 number of dielectric boundary points 3050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2276 ## 239 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7943948E-09 -1.6148489E-09 midg,1,midg; midg,igrid,midg 7.5918747E-09 -2.1524198E-09 1,midg,midg; igrid,midg,midg 1.4219895E-08 -3.5981815E-09 gauss-seidel spectral radius is 0.9853652 estimated iterations to convergence 68 setup time was (sec) 0.5900000 now iterating at: 01:44:45 rms-change max change #iterations 0.1074423 17.07148 at 10iterations 9.4767883E-03 1.670982 at 20iterations 1.2713252E-03 0.2680359 at 30iterations 2.9642583E-04 6.9599152E-02 at 40iterations 7.5491007E-05 1.8264771E-02 at 50iterations finished qdiffx linear iterations at : 01:44:49 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 7.5491007E-05 1.8264771E-02 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 01:44:49 4.453u 0.379s 0:05.33 90.4% 0+0k 0+0io 4pf+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 01:44:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2692 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: 1.783627 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): 17.98400 77.86200 ymin,ymax (A): -11.27900 44.51800 zmin,zma (A): -7.658000 35.10900 x,y,z range (A): 59.87800 55.79700 42.76700 scale (grids/A): 1.783627 object centre (A): 47.92300 16.61950 13.72550 number of atom coordinates read : 2692 total number of charged atoms : 2549 net assigned charge : 7.500022 assigned positive charge : 408.0256 centred at (gu) : 85.30457 89.31248 89.66946 assigned negative charge : -400.5264 centred at (gu) : 86.01950 89.76151 90.06168 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68058 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22740 grid for indexing accessible points = 1.400000 m= 22999 mr = 47333 m= 3229 mr = 16914 m= 136 mr = 2028 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 4950 time to turn everything in is 0.5600000 number of dielectric boundary points 28113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19869 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) : 0.5945423 object centre at (A) : 47.92300 16.61950 13.72550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2266354E-02 4.3999976E-03 midg,1,midg; midg,igrid,midg 2.8841224E-02 -2.1557620E-02 1,midg,midg; igrid,midg,midg 3.8142707E-03 -5.0755409E-03 gauss-seidel spectral radius is 0.9984524 estimated iterations to convergence 202 setup time was (sec) 0.8400000 now iterating at: 01:44:51 rms-change max change #iterations 3.765117 165.3257 at 10iterations 1.675251 61.10391 at 20iterations 0.7446648 26.59116 at 30iterations 0.3314333 12.11744 at 40iterations 0.1485950 5.106174 at 50iterations 6.6129409E-02 2.301926 at 60iterations 2.9693058E-02 1.124794 at 70iterations 1.3370159E-02 0.4698639 at 80iterations 6.1386460E-03 0.2284889 at 90iterations 2.8782745E-03 0.1104908 at 100iterations 1.4299129E-03 6.6493988E-02 at 110iterations 7.5096887E-04 3.0658722E-02 at 120iterations finished qdiffx linear iterations at : 01:45:00 total time elapsed so far: 10.13000 # loops : 120 mean,max change (kT/e) : 7.5096887E-04 3.0658722E-02 energy calculations done at 10.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.29000 DelPhi exited at 01:45:00 10.298u 0.451s 0:11.09 96.8% 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 Tue Oct 11 2011 at 01:45:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2692 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: 2.675440 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): 17.98400 77.86200 ymin,ymax (A): -11.27900 44.51800 zmin,zma (A): -7.658000 35.10900 x,y,z range (A): 59.87800 55.79700 42.76700 scale (grids/A): 2.675440 object centre (A): 47.92300 16.61950 13.72550 number of atom coordinates read : 2692 total number of charged atoms : 2549 net assigned charge : 7.500022 assigned positive charge : 408.0256 centred at (gu) : 82.95676 88.96854 89.50390 assigned negative charge : -400.5264 centred at (gu) : 84.02915 89.64222 90.09253 start vw surface at 0.1200000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 158108 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22740 grid for indexing accessible points = 1.400000 m= 76849 mr = 115319 m= 25736 mr = 62957 m= 5433 mr = 20568 m= 608 mr = 4112 m= 13 mr = 399 m= 0 mr = 2 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 16864 time to turn everything in is 1.410000 number of dielectric boundary points 63390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 20391 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) : 1.783627 object centre at (A) : 47.92300 16.61950 13.72550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2366746 4.7584675E-02 midg,1,midg; midg,igrid,midg 0.3617227 -0.4233055 1,midg,midg; igrid,midg,midg -1.2802188E-02 9.6417427E-02 gauss-seidel spectral radius is 0.9992052 estimated iterations to convergence 280 setup time was (sec) 1.730000 now iterating at: 01:45:03 rms-change max change #iterations 9.074957 330.4399 at 10iterations 5.178208 134.1221 at 20iterations 2.920058 60.50671 at 30iterations 1.653865 33.29815 at 40iterations 0.9326910 20.09222 at 50iterations 0.5248608 10.93399 at 60iterations 0.2956043 5.533139 at 70iterations 0.1666470 3.618095 at 80iterations 9.3848519E-02 1.933294 at 90iterations 5.2934229E-02 1.001319 at 100iterations 2.9838974E-02 0.6427383 at 110iterations 1.6887901E-02 0.3602257 at 120iterations 9.6117621E-03 0.2054901 at 130iterations 5.4939319E-03 0.1193390 at 140iterations 3.1994774E-03 6.8546295E-02 at 150iterations 1.9153367E-03 4.5757294E-02 at 160iterations 1.1961111E-03 3.1890869E-02 at 170iterations 7.8569114E-04 2.0694733E-02 at 180iterations finished qdiffx linear iterations at : 01:45:18 total time elapsed so far: 17.03000 # loops : 180 mean,max change (kT/e) : 7.8569114E-04 2.0694733E-02 energy calculations done at 17.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.19000 DelPhi exited at 01:45:19 17.195u 0.481s 0:18.19 97.1% 0+0k 0+0io 0pf+0w