Sat Oct 15 13:54:33 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 15 2011 at 13:54:34 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: HIZ 69 has a net charge of 0.2000 !!! WARNING: HIZ 84 has a net charge of 0.2000 !!! WARNING: HIY 97 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: HIZ 123 has a net charge of 0.2000 !!! WARNING: HIZ 129 has a net charge of 0.2000 !!! WARNING: GLU 164 has a net charge of -2.0000 !!! WARNING: HIZ 233 has a net charge of 0.2000 !!! WARNING: HIZ 248 has a net charge of 0.2000 !!! WARNING: HIY 261 has a net charge of 0.2000 !!! WARNING: ZN3 331 has a net charge of 1.4000 !!! WARNING: ZN3 333 has a net charge of 1.4000 !!! WARNING: ZN3 334 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6324279 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): -27.45600 28.83500 ymin,ymax (A): -2.973000 38.01100 zmin,zma (A): 27.73900 78.70500 x,y,z range (A): 56.29100 40.98400 50.96600 scale (grids/A): 0.6324279 object centre (A): 0.6895008 17.51900 53.22200 number of atom coordinates read : 1970 total number of charged atoms : 1839 net assigned charge : -3.999986 assigned positive charge : 281.8794 centred at (gu) : 88.11386 89.81300 90.49151 assigned negative charge : -285.8791 centred at (gu) : 87.99652 89.97232 90.46301 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5306 nv = 96 ne = 84 npr = 41006 no. pairs analyzed = 41006 no. exposed pairs = 2593 no. arc points = 18795 no. surface atoms = 879 nbur = 1091 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 251 mr = 2663 m= 4 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1748 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6240 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8446128E-09 -2.7884630E-09 midg,1,midg; midg,igrid,midg 6.6471135E-09 -1.5131301E-08 1,midg,midg; igrid,midg,midg -1.9275683E-08 2.2806141E-09 gauss-seidel spectral radius is 0.9869992 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 13:54:34 rms-change max change #iterations 0.1228046 21.36738 at 10iterations 1.1868200E-02 2.101040 at 20iterations 1.1034961E-03 0.1753755 at 30iterations 1.0478837E-04 1.8325806E-02 at 40iterations 1.0207898E-05 1.7089844E-03 at 50iterations finished qdiffx linear iterations at : 13:54:38 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 1.0207898E-05 1.7089844E-03 energy calculations done at 3.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.920000 DelPhi exited at 13:54:38 3.919u 0.243s 0:04.57 90.8% 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 15 2011 at 13:54:38 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: HIZ 69 has a net charge of 0.2000 !!! WARNING: HIZ 84 has a net charge of 0.2000 !!! WARNING: HIY 97 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: HIZ 123 has a net charge of 0.2000 !!! WARNING: HIZ 129 has a net charge of 0.2000 !!! WARNING: GLU 164 has a net charge of -2.0000 !!! WARNING: HIZ 233 has a net charge of 0.2000 !!! WARNING: HIZ 248 has a net charge of 0.2000 !!! WARNING: HIY 261 has a net charge of 0.2000 !!! WARNING: ZN3 331 has a net charge of 1.4000 !!! WARNING: ZN3 333 has a net charge of 1.4000 !!! WARNING: ZN3 334 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.897284 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): -27.45600 28.83500 ymin,ymax (A): -2.973000 38.01100 zmin,zma (A): 27.73900 78.70500 x,y,z range (A): 56.29100 40.98400 50.96600 scale (grids/A): 1.897284 object centre (A): 0.6895008 17.51900 53.22200 number of atom coordinates read : 1970 total number of charged atoms : 1839 net assigned charge : -3.999986 assigned positive charge : 281.8794 centred at (gu) : 84.34187 89.43938 91.47462 assigned negative charge : -285.8791 centred at (gu) : 83.98956 89.91697 91.38924 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 56667 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18795 grid for indexing accessible points = 1.400000 m= 18010 mr = 37012 m= 2325 mr = 12466 m= 112 mr = 1326 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 1195 time to turn everything in is 0.3000000 number of dielectric boundary points 26272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14455 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) : 0.6324279 object centre at (A) : 0.6895008 17.51900 53.22200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6514435E-02 -2.1733671E-02 midg,1,midg; midg,igrid,midg 4.9906089E-03 -1.0464166E-02 1,midg,midg; igrid,midg,midg -2.4020325E-03 2.0895392E-02 gauss-seidel spectral radius is 0.9985669 estimated iterations to convergence 209 setup time was (sec) 0.5700000 now iterating at: 13:54:39 rms-change max change #iterations 3.559660 184.2689 at 10iterations 1.632681 62.78495 at 20iterations 0.7484059 27.80338 at 30iterations 0.3426124 13.02743 at 40iterations 0.1579113 5.602760 at 50iterations 7.2426289E-02 2.596303 at 60iterations 3.3099916E-02 1.263033 at 70iterations 1.5232291E-02 0.5061035 at 80iterations 6.9684768E-03 0.2624289 at 90iterations 3.2126538E-03 0.1111869 at 100iterations 1.4656693E-03 5.2833557E-02 at 110iterations 6.7534106E-04 2.3834229E-02 at 120iterations finished qdiffx linear iterations at : 13:54:47 total time elapsed so far: 8.830000 # loops : 120 mean,max change (kT/e) : 6.7534106E-04 2.3834229E-02 energy calculations done at 8.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.960000 DelPhi exited at 13:54:48 8.962u 0.277s 0:09.56 96.5% 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 15 2011 at 13:54:48 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: HIZ 69 has a net charge of 0.2000 !!! WARNING: HIZ 84 has a net charge of 0.2000 !!! WARNING: HIY 97 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: HIZ 123 has a net charge of 0.2000 !!! WARNING: HIZ 129 has a net charge of 0.2000 !!! WARNING: GLU 164 has a net charge of -2.0000 !!! WARNING: HIZ 233 has a net charge of 0.2000 !!! WARNING: HIZ 248 has a net charge of 0.2000 !!! WARNING: HIY 261 has a net charge of 0.2000 !!! WARNING: ZN3 331 has a net charge of 1.4000 !!! WARNING: ZN3 333 has a net charge of 1.4000 !!! WARNING: ZN3 334 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.845926 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): -27.45600 28.83500 ymin,ymax (A): -2.973000 38.01100 zmin,zma (A): 27.73900 78.70500 x,y,z range (A): 56.29100 40.98400 50.96600 scale (grids/A): 2.845926 object centre (A): 0.6895008 17.51900 53.22200 number of atom coordinates read : 1970 total number of charged atoms : 1839 net assigned charge : -3.999986 assigned positive charge : 281.8794 centred at (gu) : 81.51288 89.15912 92.21194 assigned negative charge : -285.8791 centred at (gu) : 80.98441 89.87543 92.08376 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 131351 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18795 grid for indexing accessible points = 1.400000 m= 60152 mr = 90632 m= 19197 mr = 47281 m= 3889 mr = 14821 m= 463 mr = 2730 m= 23 mr = 300 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 4207 time to turn everything in is 0.7700000 number of dielectric boundary points 59308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 14707 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) : 1.897284 object centre at (A) : 0.6895008 17.51900 53.22200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6713068 -0.2779939 midg,1,midg; midg,igrid,midg 2.8606338E-02 -7.9068579E-02 1,midg,midg; igrid,midg,midg -0.3091279 0.3329737 gauss-seidel spectral radius is 0.9992394 estimated iterations to convergence 286 setup time was (sec) 1.050000 now iterating at: 13:54:49 rms-change max change #iterations 8.429710 344.5986 at 10iterations 4.879394 126.9613 at 20iterations 2.811649 59.64867 at 30iterations 1.619095 38.65678 at 40iterations 0.9289870 22.00185 at 50iterations 0.5313693 11.58918 at 60iterations 0.3041907 7.422497 at 70iterations 0.1730560 3.623407 at 80iterations 9.8993830E-02 2.135458 at 90iterations 5.6365199E-02 1.087683 at 100iterations 3.2152452E-02 0.6766663 at 110iterations 1.8302662E-02 0.3814263 at 120iterations 1.0433173E-02 0.2496691 at 130iterations 5.9374277E-03 0.1193542 at 140iterations 3.3842993E-03 6.7939758E-02 at 150iterations 1.9222914E-03 3.8137436E-02 at 160iterations 1.0950143E-03 2.3395538E-02 at 170iterations 6.2545715E-04 1.3635159E-02 at 180iterations finished qdiffx linear iterations at : 13:55:02 total time elapsed so far: 14.38000 # loops : 180 mean,max change (kT/e) : 6.2545715E-04 1.3635159E-02 energy calculations done at 14.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.52000 DelPhi exited at 13:55:03 14.517u 0.309s 0:15.26 97.0% 0+0k 0+0io 0pf+0w