Sat Oct 8 20:44:58 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 20:44:58 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN3 357 has a net charge of 1.4000 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: 0.6270476 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): -11.20700 38.78300 ymin,ymax (A): -21.90800 24.67700 zmin,zma (A): -12.11200 44.66200 x,y,z range (A): 49.99000 46.58500 56.77400 scale (grids/A): 0.6270476 object centre (A): 13.78800 1.384501 16.27500 number of atom coordinates read : 2584 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.73382 89.25606 89.72979 assigned negative charge : -387.4045 centred at (gu) : 88.63029 89.30412 89.60408 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6598 nv = 96 ne = 84 npr = 53868 no. pairs analyzed = 53868 no. exposed pairs = 3095 no. arc points = 21864 no. surface atoms = 1034 nbur = 1550 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 305 mr = 3631 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 0.3000000 number of dielectric boundary points 3236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2121 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8183 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6243211E-09 1.3341158E-08 midg,1,midg; midg,igrid,midg 9.3819210E-09 1.9153835E-10 1,midg,midg; igrid,midg,midg -5.8994414E-09 9.4242258E-09 gauss-seidel spectral radius is 0.9868199 estimated iterations to convergence 71 setup time was (sec) 0.5300000 now iterating at: 20:44:59 rms-change max change #iterations 0.1305969 17.14211 at 10iterations 1.2639184E-02 1.863745 at 20iterations 1.4046002E-03 0.2451134 at 30iterations 2.9492922E-04 5.7731628E-02 at 40iterations 9.2992588E-05 1.9554138E-02 at 50iterations finished qdiffx linear iterations at : 20:45:01 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 9.2992588E-05 1.9554138E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 20:45:02 3.316u 0.173s 0:03.79 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 Sat Oct 8 2011 at 20:45:02 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN3 357 has a net charge of 1.4000 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: 1.881143 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): -11.20700 38.78300 ymin,ymax (A): -21.90800 24.67700 zmin,zma (A): -12.11200 44.66200 x,y,z range (A): 49.99000 46.58500 56.77400 scale (grids/A): 1.881143 object centre (A): 13.78800 1.384501 16.27500 number of atom coordinates read : 2584 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 86.20097 87.76807 89.18892 assigned negative charge : -387.4045 centred at (gu) : 85.89051 87.91223 88.81222 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71561 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21864 grid for indexing accessible points = 1.400000 m= 24777 mr = 49922 m= 3703 mr = 18106 m= 179 mr = 2284 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2608 time to turn everything in is 0.5000000 number of dielectric boundary points 29862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 19301 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) : 0.6270476 object centre at (A) : 13.78800 1.384501 16.27500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4938950E-02 2.1846600E-02 midg,1,midg; midg,igrid,midg 1.2890592E-02 1.2987790E-03 1,midg,midg; igrid,midg,midg -6.1780293E-03 3.8006604E-02 gauss-seidel spectral radius is 0.9985957 estimated iterations to convergence 212 setup time was (sec) 0.7500000 now iterating at: 20:45:03 rms-change max change #iterations 4.110834 169.0188 at 10iterations 1.906406 75.87698 at 20iterations 0.8802515 28.05488 at 30iterations 0.4081927 14.55767 at 40iterations 0.1893419 6.816403 at 50iterations 8.7729521E-02 2.741378 at 60iterations 4.0685099E-02 1.584274 at 70iterations 1.8957946E-02 0.6155014 at 80iterations 8.8186078E-03 0.2657323 at 90iterations 4.1348501E-03 0.1499538 at 100iterations 1.9678096E-03 6.0432434E-02 at 110iterations 9.6829032E-04 3.4888268E-02 at 120iterations finished qdiffx linear iterations at : 20:45:09 total time elapsed so far: 6.850000 # loops : 120 mean,max change (kT/e) : 9.6829032E-04 3.4888268E-02 energy calculations done at 6.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.030000 DelPhi exited at 20:45:09 7.030u 0.195s 0:07.53 95.8% 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 Sat Oct 8 2011 at 20:45:09 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN3 357 has a net charge of 1.4000 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: 2.821714 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): -11.20700 38.78300 ymin,ymax (A): -21.90800 24.67700 zmin,zma (A): -12.11200 44.66200 x,y,z range (A): 49.99000 46.58500 56.77400 scale (grids/A): 2.821714 object centre (A): 13.78800 1.384501 16.27500 number of atom coordinates read : 2584 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 84.30133 86.65198 88.78318 assigned negative charge : -387.4045 centred at (gu) : 83.83565 86.86826 88.21819 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 165880 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21864 grid for indexing accessible points = 1.400000 m= 82208 mr = 121101 m= 27926 mr = 67232 m= 6495 mr = 22119 m= 849 mr = 4933 m= 32 mr = 527 m= 0 mr = 13 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 8795 time to turn everything in is 1.240000 number of dielectric boundary points 67465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 19631 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) : 1.881143 object centre at (A) : 13.78800 1.384501 16.27500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0659582E-02 0.2328636 midg,1,midg; midg,igrid,midg 0.1590883 -4.8264475E-03 1,midg,midg; igrid,midg,midg -6.6400714E-02 0.4777792 gauss-seidel spectral radius is 0.9992424 estimated iterations to convergence 287 setup time was (sec) 1.510000 now iterating at: 20:45:11 rms-change max change #iterations 9.642479 278.9049 at 10iterations 5.574456 130.3880 at 20iterations 3.196874 67.74005 at 30iterations 1.835583 38.89443 at 40iterations 1.051811 20.79494 at 50iterations 0.6023231 11.21173 at 60iterations 0.3452987 6.317160 at 70iterations 0.1974537 4.108826 at 80iterations 0.1128768 2.044480 at 90iterations 6.4560160E-02 1.240120 at 100iterations 3.6879767E-02 0.6385345 at 110iterations 2.1079989E-02 0.4303336 at 120iterations 1.2031878E-02 0.2315178 at 130iterations 6.9141705E-03 0.1281948 at 140iterations 3.9539272E-03 8.4083557E-02 at 150iterations 2.2720697E-03 4.2566299E-02 at 160iterations 1.3150541E-03 2.7275085E-02 at 170iterations 7.7390438E-04 1.5544891E-02 at 180iterations finished qdiffx linear iterations at : 20:45:21 total time elapsed so far: 11.06000 # loops : 180 mean,max change (kT/e) : 7.7390438E-04 1.5544891E-02 energy calculations done at 11.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.23000 DelPhi exited at 20:45:21 11.231u 0.181s 0:11.70 97.5% 0+0k 0+0io 0pf+0w