Sat Oct 15 15:28:11 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 15:28:11 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 = 4781 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5098752 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): 35.99700 105.8180 ymin,ymax (A): 5.653000 65.66800 zmin,zma (A): -13.01700 47.33500 x,y,z range (A): 69.82100 60.01500 60.35201 scale (grids/A): 0.5098752 object centre (A): 70.90750 35.66050 17.15900 number of atom coordinates read : 4781 total number of charged atoms : 4611 net assigned charge : -6.499988 assigned positive charge : 748.5333 centred at (gu) : 90.58006 88.94952 89.32515 assigned negative charge : -755.0377 centred at (gu) : 90.70533 89.12945 89.40314 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7749 nv = 96 ne = 84 npr = 93762 no. pairs analyzed = 93762 no. exposed pairs = 6538 no. arc points = 44901 no. surface atoms = 2177 nbur = 2604 mkacc time = 0.1600000 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 = 1.680000 m= 264 mr = 3692 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4404 ## 654 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10534 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3453709E-10 -2.5339200E-10 midg,1,midg; midg,igrid,midg 4.9652793E-10 -4.4140974E-10 1,midg,midg; igrid,midg,midg 1.9967099E-10 -5.0400972E-10 gauss-seidel spectral radius is 0.9803289 estimated iterations to convergence 59 setup time was (sec) 0.5100000 now iterating at: 15:28:11 rms-change max change #iterations 7.0101008E-02 11.17374 at 10iterations 4.1589895E-03 0.6121597 at 20iterations 4.9228437E-04 6.8596840E-02 at 30iterations 1.3220849E-04 1.6515732E-02 at 40iterations 4.2577922E-05 5.1307678E-03 at 50iterations finished qdiffx linear iterations at : 15:28:14 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 4.2577922E-05 5.1307678E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 15:28:15 3.611u 0.212s 0:04.13 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 Sat Oct 15 2011 at 15:28:15 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 = 4781 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.529626 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): 35.99700 105.8180 ymin,ymax (A): 5.653000 65.66800 zmin,zma (A): -13.01700 47.33500 x,y,z range (A): 69.82100 60.01500 60.35201 scale (grids/A): 1.529626 object centre (A): 70.90750 35.66050 17.15900 number of atom coordinates read : 4781 total number of charged atoms : 4611 net assigned charge : -6.499988 assigned positive charge : 748.5333 centred at (gu) : 91.73882 86.84730 87.97417 assigned negative charge : -755.0377 centred at (gu) : 92.11545 87.38786 88.20926 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 85136 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44901 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25068 mr = 55197 m= 2175 mr = 16175 m= 54 mr = 887 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 40174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 589 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 34605 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) : 0.5098752 object centre at (A) : 70.90750 35.66050 17.15900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7523584E-03 -4.4448334E-03 midg,1,midg; midg,igrid,midg 2.4492121E-03 -9.7417990E-03 1,midg,midg; igrid,midg,midg -7.7299154E-03 -3.6655851E-02 gauss-seidel spectral radius is 0.9981065 estimated iterations to convergence 183 setup time was (sec) 0.6300000 now iterating at: 15:28:16 rms-change max change #iterations 3.908897 161.5759 at 10iterations 1.582601 56.37812 at 20iterations 0.6470773 20.94302 at 30iterations 0.2645288 9.085684 at 40iterations 0.1081750 4.335741 at 50iterations 4.4254974E-02 1.507751 at 60iterations 1.8147752E-02 0.5491085 at 70iterations 7.4327677E-03 0.2743378 at 80iterations 3.0688287E-03 9.3883514E-02 at 90iterations 1.2775672E-03 3.8954735E-02 at 100iterations 5.4740952E-04 1.8676758E-02 at 110iterations 2.4538510E-04 7.4615479E-03 at 120iterations finished qdiffx linear iterations at : 15:28:23 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.4538510E-04 7.4615479E-03 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 15:28:23 7.953u 0.211s 0:08.47 96.3% 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 Sat Oct 15 2011 at 15:28:23 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 = 4781 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.294439 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): 35.99700 105.8180 ymin,ymax (A): 5.653000 65.66800 zmin,zma (A): -13.01700 47.33500 x,y,z range (A): 69.82100 60.01500 60.35201 scale (grids/A): 2.294439 object centre (A): 70.90750 35.66050 17.15900 number of atom coordinates read : 4781 total number of charged atoms : 4611 net assigned charge : -6.499988 assigned positive charge : 748.5333 centred at (gu) : 92.60764 85.27062 86.96085 assigned negative charge : -755.0377 centred at (gu) : 93.17300 86.08163 87.31382 start vw surface at 0.1200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 198205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44901 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 87262 mr = 136825 m= 23343 mr = 66025 m= 3125 mr = 16744 m= 142 mr = 1820 m= 4 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.010000 number of dielectric boundary points 90644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 36776 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) : 1.529626 object centre at (A) : 70.90750 35.66050 17.15900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6214890E-02 -0.1146051 midg,1,midg; midg,igrid,midg -6.2247440E-02 -0.1082750 1,midg,midg; igrid,midg,midg -0.2674274 -1.050799 gauss-seidel spectral radius is 0.9991649 estimated iterations to convergence 273 setup time was (sec) 1.260000 now iterating at: 15:28:25 rms-change max change #iterations 10.72843 318.1247 at 10iterations 6.228199 163.3976 at 20iterations 3.573963 74.91450 at 30iterations 2.044731 43.93481 at 40iterations 1.160034 22.95183 at 50iterations 0.6549345 13.51136 at 60iterations 0.3692995 7.919043 at 70iterations 0.2075509 4.082349 at 80iterations 0.1165100 2.370604 at 90iterations 6.5230340E-02 1.395446 at 100iterations 3.6436815E-02 0.6981239 at 110iterations 2.0351596E-02 0.3856859 at 120iterations 1.1368698E-02 0.2165489 at 130iterations 6.3457806E-03 0.1355896 at 140iterations 3.5471262E-03 8.0389023E-02 at 150iterations 1.9746453E-03 3.7609100E-02 at 160iterations 1.1003981E-03 2.0370483E-02 at 170iterations 6.1601988E-04 1.1717796E-02 at 180iterations finished qdiffx linear iterations at : 15:28:42 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 6.1601988E-04 1.1717796E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 15:28:42 12.879u 0.209s 0:18.87 69.2% 0+0k 0+0io 0pf+0w