Sat Oct 8 15:15:14 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 Sat Oct 8 2011 at 15:15:14 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1580 !!! WARNING: HIR 183 has a net charge of 0.5140 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: 0.6325178 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): -60.92300 -4.640000 ymin,ymax (A): -25.45800 7.824000 zmin,zma (A): -1.788000 42.68500 x,y,z range (A): 56.28300 33.28200 44.47300 scale (grids/A): 0.6325178 object centre (A): -32.78150 -8.817000 20.44850 number of atom coordinates read : 1580 total number of charged atoms : 1514 net assigned charge : 4.513999 assigned positive charge : 235.0265 centred at (gu) : 90.51591 90.02011 88.14420 assigned negative charge : -230.5123 centred at (gu) : 90.59560 90.00539 88.04792 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4440 nv = 96 ne = 84 npr = 29959 no. pairs analyzed = 29959 no. exposed pairs = 2108 no. arc points = 15100 no. surface atoms = 719 nbur = 861 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 224 mr = 2262 m= 1 mr = 25 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 0.2100000 number of dielectric boundary points 2378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1464 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 5224 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5527627E-10 7.2546946E-09 midg,1,midg; midg,igrid,midg 4.5649231E-09 6.2625838E-09 1,midg,midg; igrid,midg,midg 8.8181995E-09 9.7106023E-10 gauss-seidel spectral radius is 0.9869682 estimated iterations to convergence 72 setup time was (sec) 0.4200000 now iterating at: 15:15:15 rms-change max change #iterations 0.1065794 18.13253 at 10iterations 1.0127168E-02 1.860298 at 20iterations 9.6208660E-04 0.1716051 at 30iterations 9.1115580E-05 1.6586304E-02 at 40iterations 8.5151314E-06 1.6336441E-03 at 50iterations finished qdiffx linear iterations at : 15:15:17 total time elapsed so far: 2.830000 # loops : 50 mean,max change (kT/e) : 8.5151314E-06 1.6336441E-03 energy calculations done at 2.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.010000 DelPhi exited at 15:15:18 3.012u 0.154s 0:03.45 91.5% 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 8 2011 at 15:15:18 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1580 !!! WARNING: HIR 183 has a net charge of 0.5140 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: 1.897553 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): -60.92300 -4.640000 ymin,ymax (A): -25.45800 7.824000 zmin,zma (A): -1.788000 42.68500 x,y,z range (A): 56.28300 33.28200 44.47300 scale (grids/A): 1.897553 object centre (A): -32.78150 -8.817000 20.44850 number of atom coordinates read : 1580 total number of charged atoms : 1514 net assigned charge : 4.513999 assigned positive charge : 235.0265 centred at (gu) : 91.54818 90.06078 84.43277 assigned negative charge : -230.5123 centred at (gu) : 91.78710 90.01647 84.14390 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 47692 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15100 grid for indexing accessible points = 1.400000 m= 16050 mr = 31502 m= 2333 mr = 11424 m= 153 mr = 1317 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 21930 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 11896 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) : 0.6325178 object centre at (A) : -32.78150 -8.817000 20.44850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2702345E-02 1.0561946E-02 midg,1,midg; midg,igrid,midg 2.3188172E-03 1.1073881E-02 1,midg,midg; igrid,midg,midg 3.3052690E-02 1.6889106E-02 gauss-seidel spectral radius is 0.9985213 estimated iterations to convergence 206 setup time was (sec) 0.6000000 now iterating at: 15:15:19 rms-change max change #iterations 3.172893 187.3203 at 10iterations 1.436739 55.58376 at 20iterations 0.6538143 28.09152 at 30iterations 0.2974635 12.42923 at 40iterations 0.1343334 4.869053 at 50iterations 6.0984626E-02 2.646198 at 60iterations 2.7739933E-02 1.021525 at 70iterations 1.2527050E-02 0.4813957 at 80iterations 5.6629432E-03 0.2353392 at 90iterations 2.5746317E-03 0.1033745 at 100iterations 1.1695190E-03 5.2919388E-02 at 110iterations 5.2906945E-04 2.1652222E-02 at 120iterations finished qdiffx linear iterations at : 15:15:24 total time elapsed so far: 6.500000 # loops : 120 mean,max change (kT/e) : 5.2906945E-04 2.1652222E-02 energy calculations done at 6.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.670000 DelPhi exited at 15:15:25 6.671u 0.176s 0:07.17 95.3% 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 8 2011 at 15:15:25 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1580 !!! WARNING: HIR 183 has a net charge of 0.5140 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: 2.846330 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): -60.92300 -4.640000 ymin,ymax (A): -25.45800 7.824000 zmin,zma (A): -1.788000 42.68500 x,y,z range (A): 56.28300 33.28200 44.47300 scale (grids/A): 2.846330 object centre (A): -32.78150 -8.817000 20.44850 number of atom coordinates read : 1580 total number of charged atoms : 1514 net assigned charge : 4.513999 assigned positive charge : 235.0265 centred at (gu) : 92.32225 90.09129 81.64926 assigned negative charge : -230.5123 centred at (gu) : 92.68069 90.02480 81.21584 start vw surface at 0.1300000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 110148 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15100 grid for indexing accessible points = 1.400000 m= 53107 mr = 76788 m= 18057 mr = 42456 m= 4025 mr = 13996 m= 570 mr = 2880 m= 51 mr = 344 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 49468 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 12111 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) : 1.897553 object centre at (A) : -32.78150 -8.817000 20.44850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1902580 0.1014777 midg,1,midg; midg,igrid,midg 9.8170917E-03 0.1362845 1,midg,midg; igrid,midg,midg 0.3270791 6.9506764E-02 gauss-seidel spectral radius is 0.9992099 estimated iterations to convergence 281 setup time was (sec) 1.140000 now iterating at: 15:15:26 rms-change max change #iterations 7.528844 375.5401 at 10iterations 4.307285 127.0960 at 20iterations 2.452342 63.60297 at 30iterations 1.397717 34.75722 at 40iterations 0.7898025 18.20160 at 50iterations 0.4479388 11.11460 at 60iterations 0.2528770 6.765333 at 70iterations 0.1432090 3.239084 at 80iterations 8.0869064E-02 1.817207 at 90iterations 4.5481615E-02 1.028080 at 100iterations 2.5647542E-02 0.6121426 at 110iterations 1.4447664E-02 0.3387146 at 120iterations 8.1436960E-03 0.1798931 at 130iterations 4.5825960E-03 9.5906496E-02 at 140iterations 2.5728722E-03 6.7977846E-02 at 150iterations 1.4485547E-03 3.5713196E-02 at 160iterations 8.1928773E-04 2.1237373E-02 at 170iterations 4.5960900E-04 1.0923505E-02 at 180iterations finished qdiffx linear iterations at : 15:15:36 total time elapsed so far: 11.19000 # loops : 180 mean,max change (kT/e) : 4.5960900E-04 1.0923505E-02 energy calculations done at 11.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.37000 DelPhi exited at 15:15:37 11.374u 0.227s 0:11.88 97.5% 0+0k 0+0io 0pf+0w