Sun Oct 9 07:16:26 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 07:16:26 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2537 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: 0.5515019 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): -5.246000 41.45700 ymin,ymax (A): 37.65300 89.36400 zmin,zma (A): -2.670000 61.88100 x,y,z range (A): 46.70300 51.71100 64.55099 scale (grids/A): 0.5515019 object centre (A): 18.10550 63.50850 29.60550 number of atom coordinates read : 2537 total number of charged atoms : 2391 net assigned charge : -9.499978 assigned positive charge : 380.6038 centred at (gu) : 90.99170 88.29607 89.43364 assigned negative charge : -390.1043 centred at (gu) : 91.17028 87.90950 89.37085 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5020 nv = 96 ne = 84 npr = 50880 no. pairs analyzed = 50880 no. exposed pairs = 3496 no. arc points = 24904 no. surface atoms = 1187 nbur = 1350 mkacc time = 0.1100000 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= 216 mr = 2375 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2900000 number of dielectric boundary points 2858 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2515 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6552 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2638393E-09 -1.8645720E-10 midg,1,midg; midg,igrid,midg -5.4130118E-09 1.2820288E-09 1,midg,midg; igrid,midg,midg 4.5345544E-10 -2.4894120E-09 gauss-seidel spectral radius is 0.9830169 estimated iterations to convergence 63 setup time was (sec) 0.5300000 now iterating at: 07:16:27 rms-change max change #iterations 7.0143200E-02 12.72234 at 10iterations 4.6952199E-03 0.8978443 at 20iterations 3.2145542E-04 5.7212830E-02 at 30iterations 2.2075264E-05 4.2734146E-03 at 40iterations 1.5821262E-06 3.1948090E-04 at 50iterations finished qdiffx linear iterations at : 07:16:30 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.5821262E-06 3.1948090E-04 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 07:16:30 3.434u 0.213s 0:03.93 92.6% 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 07:16:30 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2537 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: 1.654506 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): -5.246000 41.45700 ymin,ymax (A): 37.65300 89.36400 zmin,zma (A): -2.670000 61.88100 x,y,z range (A): 46.70300 51.71100 64.55099 scale (grids/A): 1.654506 object centre (A): 18.10550 63.50850 29.60550 number of atom coordinates read : 2537 total number of charged atoms : 2391 net assigned charge : -9.499978 assigned positive charge : 380.6038 centred at (gu) : 92.97433 84.88754 88.30050 assigned negative charge : -390.1043 centred at (gu) : 93.51032 83.72836 88.11236 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 55516 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24904 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15846 mr = 35369 m= 1464 mr = 10472 m= 33 mr = 604 m= 0 mr = 3 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 834 time to turn everything in is 0.4300000 number of dielectric boundary points 26411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 274 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 18361 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) : 0.5515019 object centre at (A) : 18.10550 63.50850 29.60550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1485703E-02 3.7617974E-03 midg,1,midg; midg,igrid,midg -3.3129815E-02 5.7654576E-03 1,midg,midg; igrid,midg,midg -3.2796750E-03 -1.6512692E-02 gauss-seidel spectral radius is 0.9981813 estimated iterations to convergence 186 setup time was (sec) 0.7300000 now iterating at: 07:16:31 rms-change max change #iterations 3.112183 163.8426 at 10iterations 1.297194 65.56463 at 20iterations 0.5381213 21.80243 at 30iterations 0.2239027 8.246719 at 40iterations 9.3386024E-02 3.591772 at 50iterations 3.8757101E-02 1.512661 at 60iterations 1.6118957E-02 0.6435547 at 70iterations 6.7021921E-03 0.2878892 at 80iterations 2.7817120E-03 0.1105976 at 90iterations 1.1552196E-03 4.6722889E-02 at 100iterations 4.8172919E-04 1.7951965E-02 at 110iterations 2.0062877E-04 7.8339577E-03 at 120iterations finished qdiffx linear iterations at : 07:16:38 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 2.0062877E-04 7.8339577E-03 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 07:16:38 7.619u 0.253s 0:08.16 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 Sun Oct 9 2011 at 07:16:38 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2537 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: 2.481759 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): -5.246000 41.45700 ymin,ymax (A): 37.65300 89.36400 zmin,zma (A): -2.670000 61.88100 x,y,z range (A): 46.70300 51.71100 64.55099 scale (grids/A): 2.481759 object centre (A): 18.10550 63.50850 29.60550 number of atom coordinates read : 2537 total number of charged atoms : 2391 net assigned charge : -9.499978 assigned positive charge : 380.6038 centred at (gu) : 94.46138 82.33128 87.45055 assigned negative charge : -390.1043 centred at (gu) : 95.26552 80.59251 87.16837 start vw surface at 0.1400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 128444 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24904 grid for indexing accessible points = 1.400000 m= 56061 mr = 86798 m= 14907 mr = 43286 m= 2082 mr = 10733 m= 120 mr = 1223 m= 3 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 2895 time to turn everything in is 0.9600000 number of dielectric boundary points 59551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 19117 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) : 1.654506 object centre at (A) : 18.10550 63.50850 29.60550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7602963 -2.2044824E-03 midg,1,midg; midg,igrid,midg -0.4799489 8.4814765E-02 1,midg,midg; igrid,midg,midg -4.7684591E-02 -0.2066962 gauss-seidel spectral radius is 0.9991288 estimated iterations to convergence 268 setup time was (sec) 1.290000 now iterating at: 07:16:40 rms-change max change #iterations 8.193124 350.5895 at 10iterations 4.572739 129.1285 at 20iterations 2.554454 87.29119 at 30iterations 1.420259 39.20369 at 40iterations 0.7846804 20.71071 at 50iterations 0.4336185 10.03207 at 60iterations 0.2389943 5.477814 at 70iterations 0.1314279 2.911390 at 80iterations 7.2264902E-02 1.533595 at 90iterations 3.9652396E-02 0.8732996 at 100iterations 2.1786610E-02 0.5129318 at 110iterations 1.1926497E-02 0.2828674 at 120iterations 6.5514878E-03 0.1720963 at 130iterations 3.5865365E-03 7.8178644E-02 at 140iterations 1.9599344E-03 4.7201633E-02 at 150iterations 1.0760543E-03 2.3735046E-02 at 160iterations 5.8847945E-04 1.5895844E-02 at 170iterations 3.2260825E-04 6.6838264E-03 at 180iterations finished qdiffx linear iterations at : 07:16:51 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 3.2260825E-04 6.6838264E-03 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.35000 DelPhi exited at 07:16:51 12.357u 0.244s 0:12.88 97.7% 0+0k 0+0io 0pf+0w