Sun Oct 9 22:34:02 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 Sun Oct 9 2011 at 22:34:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 !!! WARNING: LYS 506 has a net charge of 1.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6335196 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): -45.81700 2.833000 ymin,ymax (A): -44.36800 8.177000 zmin,zma (A): -10.12500 46.06900 x,y,z range (A): 48.65000 52.54500 56.19400 scale (grids/A): 0.6335196 object centre (A): -21.49200 -18.09550 17.97200 number of atom coordinates read : 2493 total number of charged atoms : 2446 net assigned charge : 6.500012 assigned positive charge : 391.2599 centred at (gu) : 88.76520 89.79080 90.75488 assigned negative charge : -384.7607 centred at (gu) : 88.83431 89.81304 90.80318 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6793 nv = 96 ne = 84 npr = 47440 no. pairs analyzed = 47440 no. exposed pairs = 3236 no. arc points = 23073 no. surface atoms = 1099 nbur = 1394 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 308 mr = 3502 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 66 time to turn everything in is 0.1900000 number of dielectric boundary points 3556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2403 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8359 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0577199E-08 3.5578180E-09 midg,1,midg; midg,igrid,midg 1.0361590E-08 5.3833102E-09 1,midg,midg; igrid,midg,midg 1.8784055E-08 8.8460950E-10 gauss-seidel spectral radius is 0.9870896 estimated iterations to convergence 72 setup time was (sec) 0.3800000 now iterating at: 22:34:03 rms-change max change #iterations 0.1360684 20.12910 at 10iterations 1.3035133E-02 2.091164 at 20iterations 1.2611868E-03 0.1967659 at 30iterations 1.2238100E-04 1.7463684E-02 at 40iterations 1.1836688E-05 1.8441677E-03 at 50iterations finished qdiffx linear iterations at : 22:34:06 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.1836688E-05 1.8441677E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 22:34:06 3.425u 0.186s 0:03.90 92.3% 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 Sun Oct 9 2011 at 22:34:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 !!! WARNING: LYS 506 has a net charge of 1.5000 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: 1.900559 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): -45.81700 2.833000 ymin,ymax (A): -44.36800 8.177000 zmin,zma (A): -10.12500 46.06900 x,y,z range (A): 48.65000 52.54500 56.19400 scale (grids/A): 1.900559 object centre (A): -21.49200 -18.09550 17.97200 number of atom coordinates read : 2493 total number of charged atoms : 2446 net assigned charge : 6.500012 assigned positive charge : 391.2599 centred at (gu) : 86.29471 89.37196 92.26389 assigned negative charge : -384.7607 centred at (gu) : 86.50260 89.43898 92.40900 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72990 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23073 grid for indexing accessible points = 1.400000 m= 24588 mr = 48938 m= 3806 mr = 17613 m= 219 mr = 2287 m= 2 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 743 time to turn everything in is 0.3700000 number of dielectric boundary points 32675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19256 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) : 0.6335196 object centre at (A) : -21.49200 -18.09550 17.97200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1255805E-03 3.0434640E-02 midg,1,midg; midg,igrid,midg 7.2906669E-03 1.8243572E-02 1,midg,midg; igrid,midg,midg 1.6186150E-02 -8.5694529E-03 gauss-seidel spectral radius is 0.9986237 estimated iterations to convergence 214 setup time was (sec) 0.5900000 now iterating at: 22:34:07 rms-change max change #iterations 4.174903 180.1355 at 10iterations 1.935188 64.41875 at 20iterations 0.9051386 30.45580 at 30iterations 0.4216057 14.87493 at 40iterations 0.1958747 6.226684 at 50iterations 9.1566034E-02 2.933847 at 60iterations 4.2561028E-02 1.314823 at 70iterations 1.9919587E-02 0.6902914 at 80iterations 9.2754504E-03 0.2834167 at 90iterations 4.3357676E-03 0.1490870 at 100iterations 2.0123532E-03 6.2971115E-02 at 110iterations 9.3734975E-04 3.0216217E-02 at 120iterations finished qdiffx linear iterations at : 22:34:14 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 9.3734975E-04 3.0216217E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 22:34:15 7.969u 0.193s 0:08.41 96.9% 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 Sun Oct 9 2011 at 22:34:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 !!! WARNING: LYS 506 has a net charge of 1.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.850838 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): -45.81700 2.833000 ymin,ymax (A): -44.36800 8.177000 zmin,zma (A): -10.12500 46.06900 x,y,z range (A): 48.65000 52.54500 56.19400 scale (grids/A): 2.850838 object centre (A): -21.49200 -18.09550 17.97200 number of atom coordinates read : 2493 total number of charged atoms : 2446 net assigned charge : 6.500012 assigned positive charge : 391.2599 centred at (gu) : 84.44205 89.05784 93.39585 assigned negative charge : -384.7607 centred at (gu) : 84.75392 89.15840 93.61362 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 168999 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23073 grid for indexing accessible points = 1.400000 m= 81092 mr = 119334 m= 27611 mr = 65120 m= 6719 mr = 21619 m= 1014 mr = 4895 m= 68 mr = 702 m= 0 mr = 34 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 2454 time to turn everything in is 0.9200000 number of dielectric boundary points 73799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 19563 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) : 1.900559 object centre at (A) : -21.49200 -18.09550 17.97200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8648133E-02 0.2663001 midg,1,midg; midg,igrid,midg -0.1061685 0.2835236 1,midg,midg; igrid,midg,midg 0.1991529 -0.1735239 gauss-seidel spectral radius is 0.9992629 estimated iterations to convergence 291 setup time was (sec) 1.170000 now iterating at: 22:34:16 rms-change max change #iterations 9.817241 370.9038 at 10iterations 5.730741 153.1682 at 20iterations 3.325935 68.66706 at 30iterations 1.921039 37.74139 at 40iterations 1.112793 21.90161 at 50iterations 0.6394289 12.72427 at 60iterations 0.3679740 7.098798 at 70iterations 0.2122350 3.806152 at 80iterations 0.1219324 2.294538 at 90iterations 6.9936678E-02 1.386452 at 100iterations 4.0232949E-02 0.7594056 at 110iterations 2.3128126E-02 0.4347286 at 120iterations 1.3277432E-02 0.2412682 at 130iterations 7.6250727E-03 0.1422062 at 140iterations 4.3801912E-03 8.0795288E-02 at 150iterations 2.5109104E-03 4.4056177E-02 at 160iterations 1.4434620E-03 2.8467059E-02 at 170iterations 8.2955341E-04 1.6263962E-02 at 180iterations finished qdiffx linear iterations at : 22:34:28 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 8.2955341E-04 1.6263962E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 22:34:28 12.798u 0.214s 0:13.28 97.8% 0+0k 0+0io 0pf+0w