Sat Oct 8 16:28:36 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 16:28:36 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2287 !!! WARNING: ASL 705 has a net charge of -0.1000 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: 0.6473787 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): 25.01400 74.48000 ymin,ymax (A): -16.03400 29.72200 zmin,zma (A): -18.72700 36.26400 x,y,z range (A): 49.46600 45.75600 54.99100 scale (grids/A): 0.6473787 object centre (A): 49.74700 6.844000 8.768500 number of atom coordinates read : 2287 total number of charged atoms : 2190 net assigned charge : 4.900006 assigned positive charge : 336.8792 centred at (gu) : 90.17831 88.57402 89.83722 assigned negative charge : -331.9799 centred at (gu) : 90.26131 88.68166 89.84451 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6420 nv = 96 ne = 84 npr = 46962 no. pairs analyzed = 46962 no. exposed pairs = 2754 no. arc points = 19200 no. surface atoms = 946 nbur = 1341 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3605 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1919 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7753 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8086081E-09 7.4631838E-09 midg,1,midg; midg,igrid,midg 2.9176212E-08 -3.3042666E-09 1,midg,midg; igrid,midg,midg 1.7914575E-08 -1.6607248E-09 gauss-seidel spectral radius is 0.9876075 estimated iterations to convergence 73 setup time was (sec) 0.6000000 now iterating at: 16:28:36 rms-change max change #iterations 0.1412496 22.63520 at 10iterations 1.4469510E-02 2.124039 at 20iterations 1.5036224E-03 0.2177835 at 30iterations 1.7869481E-04 2.9568672E-02 at 40iterations 2.9176479E-05 5.3176880E-03 at 50iterations finished qdiffx linear iterations at : 16:28:40 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 2.9176479E-05 5.3176880E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 16:28:40 4.187u 0.281s 0:04.76 93.6% 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 16:28:40 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2287 !!! WARNING: ASL 705 has a net charge of -0.1000 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: 1.942136 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): 25.01400 74.48000 ymin,ymax (A): -16.03400 29.72200 zmin,zma (A): -18.72700 36.26400 x,y,z range (A): 49.46600 45.75600 54.99100 scale (grids/A): 1.942136 object centre (A): 49.74700 6.844000 8.768500 number of atom coordinates read : 2287 total number of charged atoms : 2190 net assigned charge : 4.900006 assigned positive charge : 336.8792 centred at (gu) : 90.53453 85.72180 89.51143 assigned negative charge : -331.9799 centred at (gu) : 90.78381 86.04480 89.53328 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 69825 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19200 grid for indexing accessible points = 1.400000 m= 25478 mr = 49330 m= 4265 mr = 19022 m= 232 mr = 2756 m= 9 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 844 time to turn everything in is 0.6100000 number of dielectric boundary points 28615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17253 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) : 0.6473787 object centre at (A) : 49.74700 6.844000 8.768500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1050293E-02 1.4403171E-02 midg,1,midg; midg,igrid,midg 2.2902807E-02 -3.4635181E-03 1,midg,midg; igrid,midg,midg 1.4217719E-02 -4.1762333E-02 gauss-seidel spectral radius is 0.9986507 estimated iterations to convergence 216 setup time was (sec) 0.9100000 now iterating at: 16:28:42 rms-change max change #iterations 4.083283 184.9341 at 10iterations 1.912076 67.88373 at 20iterations 0.8985878 29.98944 at 30iterations 0.4240242 13.80825 at 40iterations 0.1985902 6.445541 at 50iterations 9.3863167E-02 3.001358 at 60iterations 4.4153832E-02 1.454086 at 70iterations 2.0750917E-02 0.8008957 at 80iterations 9.8123727E-03 0.3149815 at 90iterations 4.6362164E-03 0.1583500 at 100iterations 2.1837191E-03 7.1006775E-02 at 110iterations 1.0290298E-03 3.2752514E-02 at 120iterations finished qdiffx linear iterations at : 16:28:50 total time elapsed so far: 9.500000 # loops : 120 mean,max change (kT/e) : 1.0290298E-03 3.2752514E-02 energy calculations done at 9.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.670000 DelPhi exited at 16:28:51 9.675u 0.367s 0:10.31 97.2% 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 16:28:51 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2287 !!! WARNING: ASL 705 has a net charge of -0.1000 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: 2.913204 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): 25.01400 74.48000 ymin,ymax (A): -16.03400 29.72200 zmin,zma (A): -18.72700 36.26400 x,y,z range (A): 49.46600 45.75600 54.99100 scale (grids/A): 2.913204 object centre (A): 49.74700 6.844000 8.768500 number of atom coordinates read : 2287 total number of charged atoms : 2190 net assigned charge : 4.900006 assigned positive charge : 336.8792 centred at (gu) : 90.80150 83.58245 89.26707 assigned negative charge : -331.9799 centred at (gu) : 91.17584 84.06715 89.29993 start vw surface at 0.1400000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 161486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19200 grid for indexing accessible points = 1.400000 m= 81778 mr = 119064 m= 30431 mr = 67539 m= 7801 mr = 24763 m= 1048 mr = 6064 m= 56 mr = 682 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 2742 time to turn everything in is 1.610000 number of dielectric boundary points 64474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 17520 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) : 1.942136 object centre at (A) : 49.74700 6.844000 8.768500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3091052 9.2276387E-02 midg,1,midg; midg,igrid,midg 0.1415197 -5.0041422E-02 1,midg,midg; igrid,midg,midg 9.6138000E-02 -0.5574179 gauss-seidel spectral radius is 0.9992544 estimated iterations to convergence 289 setup time was (sec) 1.940000 now iterating at: 16:28:53 rms-change max change #iterations 9.394436 392.4211 at 10iterations 5.486066 132.9578 at 20iterations 3.177371 64.35950 at 30iterations 1.843913 47.68195 at 40iterations 1.067904 23.72411 at 50iterations 0.6163729 13.81333 at 60iterations 0.3559110 6.550037 at 70iterations 0.2047277 4.159997 at 80iterations 0.1181917 2.130641 at 90iterations 6.7951448E-02 1.195927 at 100iterations 3.9045788E-02 0.7091503 at 110iterations 2.2462992E-02 0.4241858 at 120iterations 1.2919571E-02 0.2655315 at 130iterations 7.4141221E-03 0.1309731 at 140iterations 4.2700125E-03 7.2479248E-02 at 150iterations 2.4629470E-03 4.4909000E-02 at 160iterations 1.4237782E-03 2.6449203E-02 at 170iterations 8.2992471E-04 1.5367508E-02 at 180iterations finished qdiffx linear iterations at : 16:29:07 total time elapsed so far: 16.13000 # loops : 180 mean,max change (kT/e) : 8.2992471E-04 1.5367508E-02 energy calculations done at 16.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.32000 DelPhi exited at 16:29:08 16.323u 0.360s 0:16.96 98.3% 0+0k 0+0io 0pf+0w