Sat Oct 8 14:38:28 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 Sat Oct 8 2011 at 14:38:28 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3042 !!! WARNING: NAP 317 has a net charge of -2.0000 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: 0.6482038 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): -30.55800 24.36300 ymin,ymax (A): -26.27800 26.10600 zmin,zma (A): -26.01600 26.82900 x,y,z range (A): 54.92100 52.38400 52.84500 scale (grids/A): 0.6482038 object centre (A): -3.097501 -8.6000443E-02 0.4065008 number of atom coordinates read : 3042 total number of charged atoms : 2895 net assigned charge : 7.1674585E-06 assigned positive charge : 454.8286 centred at (gu) : 91.46525 90.26306 89.75591 assigned negative charge : -454.8293 centred at (gu) : 91.37727 90.33698 89.78560 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8401 nv = 96 ne = 84 npr = 64177 no. pairs analyzed = 64177 no. exposed pairs = 3472 no. arc points = 24032 no. surface atoms = 1178 nbur = 1864 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 399 mr = 4919 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2302 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10229 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0855817E-09 -5.0081028E-09 midg,1,midg; midg,igrid,midg 1.1592057E-08 -1.3644674E-08 1,midg,midg; igrid,midg,midg -1.1198390E-08 2.0110953E-08 gauss-seidel spectral radius is 0.9876987 estimated iterations to convergence 74 setup time was (sec) 0.6600000 now iterating at: 14:38:29 rms-change max change #iterations 0.1717241 21.50011 at 10iterations 1.7917057E-02 2.624210 at 20iterations 1.9013155E-03 0.2530172 at 30iterations 2.1678851E-04 2.7642250E-02 at 40iterations 2.7929771E-05 3.3836365E-03 at 50iterations finished qdiffx linear iterations at : 14:38:33 total time elapsed so far: 4.510000 # loops : 50 mean,max change (kT/e) : 2.7929771E-05 3.3836365E-03 energy calculations done at 4.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.680000 DelPhi exited at 14:38:33 4.686u 0.405s 0:05.46 93.0% 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 14:38:33 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3042 !!! WARNING: NAP 317 has a net charge of -2.0000 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: 1.944611 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): -30.55800 24.36300 ymin,ymax (A): -26.27800 26.10600 zmin,zma (A): -26.01600 26.82900 x,y,z range (A): 54.92100 52.38400 52.84500 scale (grids/A): 1.944611 object centre (A): -3.097501 -8.6000443E-02 0.4065008 number of atom coordinates read : 3042 total number of charged atoms : 2895 net assigned charge : 7.1674585E-06 assigned positive charge : 454.8286 centred at (gu) : 94.39532 90.78849 89.26719 assigned negative charge : -454.8293 centred at (gu) : 94.13145 91.01076 89.35644 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 91626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24032 grid for indexing accessible points = 1.400000 m= 32969 mr = 66290 m= 4987 mr = 24897 m= 285 mr = 3159 m= 4 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 114 time to turn everything in is 0.7300000 number of dielectric boundary points 35421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 22811 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) : 0.6482038 object centre at (A) : -3.097501 -8.6000443E-02 0.4065008 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9600775E-03 -1.4378175E-02 midg,1,midg; midg,igrid,midg 1.5526002E-02 2.5383297E-02 1,midg,midg; igrid,midg,midg -2.8377723E-02 2.3884276E-02 gauss-seidel spectral radius is 0.9987221 estimated iterations to convergence 222 setup time was (sec) 1.030000 now iterating at: 14:38:35 rms-change max change #iterations 4.879497 221.9962 at 10iterations 2.354592 69.97263 at 20iterations 1.126619 32.41611 at 30iterations 0.5425237 15.85847 at 40iterations 0.2605326 7.183411 at 50iterations 0.1249386 3.598450 at 60iterations 6.0238037E-02 1.683187 at 70iterations 2.8993312E-02 0.8952360 at 80iterations 1.3950506E-02 0.3932284 at 90iterations 6.7288252E-03 0.2104645 at 100iterations 3.2343189E-03 0.1096210 at 110iterations 1.5570367E-03 4.7349930E-02 at 120iterations finished qdiffx linear iterations at : 14:38:44 total time elapsed so far: 10.86000 # loops : 120 mean,max change (kT/e) : 1.5570367E-03 4.7349930E-02 energy calculations done at 10.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.04000 DelPhi exited at 14:38:45 11.042u 0.470s 0:11.80 97.5% 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 Sat Oct 8 2011 at 14:38:45 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3042 !!! WARNING: NAP 317 has a net charge of -2.0000 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: 2.916917 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): -30.55800 24.36300 ymin,ymax (A): -26.27800 26.10600 zmin,zma (A): -26.01600 26.82900 x,y,z range (A): 54.92100 52.38400 52.84500 scale (grids/A): 2.916917 object centre (A): -3.097501 -8.6000443E-02 0.4065008 number of atom coordinates read : 3042 total number of charged atoms : 2895 net assigned charge : 7.1674585E-06 assigned positive charge : 454.8286 centred at (gu) : 96.59283 91.18285 88.90071 assigned negative charge : -454.8293 centred at (gu) : 96.19707 91.51614 89.03451 start vw surface at 0.1300000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 212457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24032 grid for indexing accessible points = 1.400000 m= 108435 mr = 160189 m= 38289 mr = 90527 m= 8729 mr = 31097 m= 1254 mr = 6647 m= 73 mr = 832 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 363 time to turn everything in is 1.950000 number of dielectric boundary points 79920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 23158 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) : 1.944611 object centre at (A) : -3.097501 -8.6000443E-02 0.4065008 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5006375E-02 -0.1227965 midg,1,midg; midg,igrid,midg 4.6050191E-02 0.3030666 1,midg,midg; igrid,midg,midg -0.1519747 0.3116382 gauss-seidel spectral radius is 0.9992819 estimated iterations to convergence 294 setup time was (sec) 2.300000 now iterating at: 14:38:48 rms-change max change #iterations 11.15728 412.6139 at 10iterations 6.560946 143.4208 at 20iterations 3.851197 77.31755 at 30iterations 2.252825 45.65668 at 40iterations 1.316403 22.57906 at 50iterations 0.7704033 13.65008 at 60iterations 0.4482586 7.544704 at 70iterations 0.2606936 4.420649 at 80iterations 0.1513935 2.602819 at 90iterations 8.8339984E-02 1.480507 at 100iterations 5.1371727E-02 0.8131485 at 110iterations 2.9786712E-02 0.4867325 at 120iterations 1.7345546E-02 0.2744370 at 130iterations 1.0091326E-02 0.1591568 at 140iterations 5.8914740E-03 9.5344543E-02 at 150iterations 3.4423072E-03 5.7667255E-02 at 160iterations 2.0232205E-03 3.6644936E-02 at 170iterations 1.1967075E-03 1.8810272E-02 at 180iterations finished qdiffx linear iterations at : 14:39:05 total time elapsed so far: 19.33000 # loops : 180 mean,max change (kT/e) : 1.1967075E-03 1.8810272E-02 energy calculations done at 19.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.50000 DelPhi exited at 14:39:05 19.501u 0.505s 0:20.29 98.5% 0+0k 0+0io 0pf+0w