Sun Oct 9 19:59:39 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 Sun Oct 9 2011 at 19:59:39 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3861 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 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: 0.5566501 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): 4.348000 66.61600 ymin,ymax (A): -1.885000 62.06900 zmin,zma (A): -1.017000 62.04900 x,y,z range (A): 62.26801 63.95400 63.06600 scale (grids/A): 0.5566501 object centre (A): 35.48200 30.09200 30.51600 number of atom coordinates read : 3861 total number of charged atoms : 3702 net assigned charge : 1.530027 assigned positive charge : 580.0652 centred at (gu) : 89.27848 88.79269 88.38961 assigned negative charge : -578.5375 centred at (gu) : 89.19518 88.93124 88.35757 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8073 nv = 96 ne = 84 npr = 75611 no. pairs analyzed = 75611 no. exposed pairs = 4961 no. arc points = 34118 no. surface atoms = 1681 nbur = 2180 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 347 mr = 4297 m= 0 mr = 12 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 4111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3482 ## 397 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 10385 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1200202E-10 3.6747250E-10 midg,1,midg; midg,igrid,midg 2.5230702E-09 -1.2300279E-09 1,midg,midg; igrid,midg,midg -1.1195708E-09 9.9369979E-10 gauss-seidel spectral radius is 0.9834297 estimated iterations to convergence 64 setup time was (sec) 0.4600000 now iterating at: 19:59:39 rms-change max change #iterations 9.4727740E-02 14.19247 at 10iterations 9.7596776E-03 1.395584 at 20iterations 4.2264601E-03 0.4806633 at 30iterations 2.5773554E-03 0.2908745 at 40iterations 1.5966891E-03 0.1806526 at 50iterations finished qdiffx linear iterations at : 19:59:42 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.5966891E-03 0.1806526 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 19:59:43 3.499u 0.175s 0:03.96 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 Sun Oct 9 2011 at 19:59:43 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3861 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 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: 1.669950 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): 4.348000 66.61600 ymin,ymax (A): -1.885000 62.06900 zmin,zma (A): -1.017000 62.04900 x,y,z range (A): 62.26801 63.95400 63.06600 scale (grids/A): 1.669950 object centre (A): 35.48200 30.09200 30.51600 number of atom coordinates read : 3861 total number of charged atoms : 3702 net assigned charge : 1.530027 assigned positive charge : 580.0652 centred at (gu) : 87.83434 86.37660 85.16758 assigned negative charge : -578.5375 centred at (gu) : 87.58499 86.79314 85.07214 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 89579 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34118 grid for indexing accessible points = 1.400000 m= 30273 mr = 62598 m= 3801 mr = 21219 m= 134 mr = 2005 m= 0 mr = 14 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 167 time to turn everything in is 0.4400000 number of dielectric boundary points 37951 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 370 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 28520 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) : 0.5566501 object centre at (A) : 35.48200 30.09200 30.51600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5497874E-02 -9.3705757E-03 midg,1,midg; midg,igrid,midg 2.1699267E-02 -9.1504725E-03 1,midg,midg; igrid,midg,midg -3.9063394E-03 6.2776096E-03 gauss-seidel spectral radius is 0.9983613 estimated iterations to convergence 196 setup time was (sec) 0.6500000 now iterating at: 19:59:43 rms-change max change #iterations 4.108065 169.1635 at 10iterations 1.793725 59.09248 at 20iterations 0.7852973 24.50427 at 30iterations 0.3439991 11.28991 at 40iterations 0.1514234 4.542347 at 50iterations 6.6944212E-02 2.124780 at 60iterations 3.0558800E-02 0.9948883 at 70iterations 1.5218597E-02 0.5240173 at 80iterations 9.0580666E-03 0.3365173 at 90iterations 6.5373625E-03 0.1867269 at 100iterations 5.2934862E-03 0.1367340 at 110iterations 4.4436175E-03 0.1075668 at 120iterations finished qdiffx linear iterations at : 19:59:51 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 4.4436175E-03 0.1075668 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 19:59:51 7.972u 0.208s 0:08.45 96.6% 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 Sun Oct 9 2011 at 19:59:51 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3861 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 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: 2.504925 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): 4.348000 66.61600 ymin,ymax (A): -1.885000 62.06900 zmin,zma (A): -1.017000 62.04900 x,y,z range (A): 62.26801 63.95400 63.06600 scale (grids/A): 2.504925 object centre (A): 35.48200 30.09200 30.51600 number of atom coordinates read : 3861 total number of charged atoms : 3702 net assigned charge : 1.530027 assigned positive charge : 580.0652 centred at (gu) : 86.75127 84.56471 82.75116 assigned negative charge : -578.5375 centred at (gu) : 86.37742 85.18961 82.60811 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 207870 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34118 grid for indexing accessible points = 1.400000 m= 102213 mr = 152701 m= 32580 mr = 81913 m= 6244 mr = 24745 m= 531 mr = 4167 m= 6 mr = 233 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 462 time to turn everything in is 1.110000 number of dielectric boundary points 85685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 29577 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) : 1.669950 object centre at (A) : 35.48200 30.09200 30.51600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5970151 -0.1938551 midg,1,midg; midg,igrid,midg 0.3442020 -0.1424019 1,midg,midg; igrid,midg,midg 2.8252683E-03 -4.4493396E-03 gauss-seidel spectral radius is 0.9992174 estimated iterations to convergence 282 setup time was (sec) 1.360000 now iterating at: 19:59:53 rms-change max change #iterations 10.68712 430.7405 at 10iterations 6.285529 171.4606 at 20iterations 3.682529 85.33192 at 30iterations 2.135361 48.72068 at 40iterations 1.232464 24.57104 at 50iterations 0.7108337 15.17238 at 60iterations 0.4075589 7.608795 at 70iterations 0.2333294 5.109634 at 80iterations 0.1336934 2.743148 at 90iterations 7.6336786E-02 1.566054 at 100iterations 4.3659847E-02 0.7839661 at 110iterations 2.4988042E-02 0.5348396 at 120iterations 1.4466910E-02 0.2915039 at 130iterations 8.5150115E-03 0.1683655 at 140iterations 5.2197324E-03 0.1102219 at 150iterations 3.4524363E-03 7.0518494E-02 at 160iterations 2.5103656E-03 4.5692444E-02 at 170iterations 2.0057256E-03 3.5110474E-02 at 180iterations finished qdiffx linear iterations at : 20:00:04 total time elapsed so far: 12.97000 # loops : 180 mean,max change (kT/e) : 2.0057256E-03 3.5110474E-02 energy calculations done at 12.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 20:00:05 13.099u 0.207s 0:13.61 97.6% 0+0k 0+0io 0pf+0w