Wed Dec 28 11:02:00 PST 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 Wed Dec 28 2011 at 11:02:01 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6472257 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): -6.559000 34.47600 ymin,ymax (A): -3.525000 48.11900 zmin,zma (A): -24.07500 30.92900 x,y,z range (A): 41.03500 51.64400 55.00400 scale (grids/A): 0.6472257 object centre (A): 13.95850 22.29700 3.427001 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 291.8020 centred at (gu) : 91.00167 92.50257 90.11805 assigned negative charge : -288.4402 centred at (gu) : 91.13164 92.66006 90.06857 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5546 nv = 96 ne = 84 npr = 40959 no. pairs analyzed = 40959 no. exposed pairs = 2404 no. arc points = 16847 no. surface atoms = 814 nbur = 1152 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 280 mr = 3121 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.2900000 number of dielectric boundary points 2675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1680 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6593 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3783453E-09 1.2026758E-08 midg,1,midg; midg,igrid,midg 1.3465305E-08 -1.7852512E-08 1,midg,midg; igrid,midg,midg 1.6162248E-08 -8.9889527E-09 gauss-seidel spectral radius is 0.9875715 estimated iterations to convergence 73 setup time was (sec) 0.6300000 now iterating at: 11:02:02 rms-change max change #iterations 0.1368160 24.11127 at 10iterations 1.3850351E-02 2.184294 at 20iterations 1.4072774E-03 0.2500181 at 30iterations 1.4204458E-04 2.0839691E-02 at 40iterations 1.4454996E-05 2.7780533E-03 at 50iterations finished qdiffx linear iterations at : 11:02:06 total time elapsed so far: 4.790000 # loops : 50 mean,max change (kT/e) : 1.4454996E-05 2.7780533E-03 energy calculations done at 4.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.980000 DelPhi exited at 11:02:09 4.982u 0.407s 0:07.95 67.6% 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 Wed Dec 28 2011 at 11:02:09 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 1.941677 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): -6.559000 34.47600 ymin,ymax (A): -3.525000 48.11900 zmin,zma (A): -24.07500 30.92900 x,y,z range (A): 41.03500 51.64400 55.00400 scale (grids/A): 1.941677 object centre (A): 13.95850 22.29700 3.427001 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 291.8020 centred at (gu) : 93.00479 97.50765 90.35400 assigned negative charge : -288.4402 centred at (gu) : 93.39522 97.98030 90.20595 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 59589 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16847 grid for indexing accessible points = 1.400000 m= 22161 mr = 41339 m= 3573 mr = 17020 m= 216 mr = 2378 m= 4 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2876 time to turn everything in is 0.5500000 number of dielectric boundary points 24703 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 14459 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) : 0.6472257 object centre at (A) : 13.95850 22.29700 3.427001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7561351E-02 1.7646635E-02 midg,1,midg; midg,igrid,midg 3.9621599E-02 -8.7262560E-03 1,midg,midg; igrid,midg,midg 1.0472323E-02 -6.8705673E-03 gauss-seidel spectral radius is 0.9986035 estimated iterations to convergence 212 setup time was (sec) 0.9000000 now iterating at: 11:02:10 rms-change max change #iterations 3.752419 166.1346 at 10iterations 1.744260 59.98410 at 20iterations 0.8123273 29.08075 at 30iterations 0.3772999 12.44592 at 40iterations 0.1749116 6.680355 at 50iterations 8.1004456E-02 2.980331 at 60iterations 3.7590817E-02 1.408663 at 70iterations 1.7488793E-02 0.5718288 at 80iterations 8.0808969E-03 0.2858582 at 90iterations 3.7675649E-03 0.1318011 at 100iterations 1.7488274E-03 6.1965942E-02 at 110iterations 8.0926396E-04 2.7672768E-02 at 120iterations finished qdiffx linear iterations at : 11:02:21 total time elapsed so far: 11.93000 # loops : 120 mean,max change (kT/e) : 8.0926396E-04 2.7672768E-02 energy calculations done at 11.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.10000 DelPhi exited at 11:02:22 12.105u 0.432s 0:13.56 92.4% 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 Wed Dec 28 2011 at 11:02:22 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 2.912516 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): -6.559000 34.47600 ymin,ymax (A): -3.525000 48.11900 zmin,zma (A): -24.07500 30.92900 x,y,z range (A): 41.03500 51.64400 55.00400 scale (grids/A): 2.912516 object centre (A): 13.95850 22.29700 3.427001 number of atom coordinates read : 1966 total number of charged atoms : 1832 net assigned charge : 3.362005 assigned positive charge : 291.8020 centred at (gu) : 94.50721 101.2615 90.53099 assigned negative charge : -288.4402 centred at (gu) : 95.09292 101.9705 90.30899 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 137582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16847 grid for indexing accessible points = 1.400000 m= 70863 mr = 99847 m= 26555 mr = 59204 m= 6520 mr = 22047 m= 996 mr = 5114 m= 65 mr = 730 m= 0 mr = 22 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 10188 time to turn everything in is 1.400000 number of dielectric boundary points 55617 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 14656 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) : 1.941677 object centre at (A) : 13.95850 22.29700 3.427001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9980155 4.5684457E-02 midg,1,midg; midg,igrid,midg 0.3855687 -0.1053780 1,midg,midg; igrid,midg,midg 7.3784634E-02 -4.1012347E-02 gauss-seidel spectral radius is 0.9992359 estimated iterations to convergence 286 setup time was (sec) 1.780000 now iterating at: 11:02:24 rms-change max change #iterations 8.760972 420.6042 at 10iterations 5.041226 131.8669 at 20iterations 2.876501 85.83195 at 30iterations 1.633966 36.92553 at 40iterations 0.9326105 19.74219 at 50iterations 0.5314527 12.47246 at 60iterations 0.3012149 5.882900 at 70iterations 0.1718550 3.714881 at 80iterations 9.7711645E-02 2.236377 at 90iterations 5.5437386E-02 1.015052 at 100iterations 3.1507067E-02 0.6228349 at 110iterations 1.7898820E-02 0.3658943 at 120iterations 1.0197200E-02 0.2194443 at 130iterations 5.7873721E-03 0.1232290 at 140iterations 3.2966656E-03 6.8667561E-02 at 150iterations 1.8693944E-03 3.9073944E-02 at 160iterations 1.0634278E-03 2.1225929E-02 at 170iterations 6.0362887E-04 1.1276245E-02 at 180iterations finished qdiffx linear iterations at : 11:02:43 total time elapsed so far: 20.10000 # loops : 180 mean,max change (kT/e) : 6.0362887E-04 1.1276245E-02 energy calculations done at 20.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.27000 DelPhi exited at 11:02:44 20.267u 0.408s 0:22.27 92.7% 0+0k 0+0io 0pf+0w