Mon Oct 10 14:14:28 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 Mon Oct 10 2011 at 14:14:28 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 = 1603 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: 0.7229014 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): -6.311000 37.18600 ymin,ymax (A): 1.020000 50.26600 zmin,zma (A): 6.184000 47.56400 x,y,z range (A): 43.49700 49.24600 41.38000 scale (grids/A): 0.7229014 object centre (A): 15.43750 25.64300 26.87400 number of atom coordinates read : 1603 total number of charged atoms : 1467 net assigned charge : -7.499990 assigned positive charge : 232.9132 centred at (gu) : 90.66727 91.53117 90.97909 assigned negative charge : -240.4131 centred at (gu) : 90.69197 91.78815 90.65226 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5777 nv = 96 ne = 84 npr = 33251 no. pairs analyzed = 33251 no. exposed pairs = 2121 no. arc points = 14829 no. surface atoms = 717 nbur = 886 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 347 mr = 3161 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.2300000 number of dielectric boundary points 2906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1172 ## 76 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6046 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2283382E-07 9.7358985E-08 midg,1,midg; midg,igrid,midg 3.1652561E-08 -3.0834570E-07 1,midg,midg; igrid,midg,midg -6.7371339E-08 -1.1583665E-07 gauss-seidel spectral radius is 0.9899817 estimated iterations to convergence 81 setup time was (sec) 0.4400000 now iterating at: 14:14:28 rms-change max change #iterations 0.1898875 28.44135 at 10iterations 2.4173871E-02 4.009022 at 20iterations 3.0881898E-03 0.4926109 at 30iterations 3.9136142E-04 6.2873840E-02 at 40iterations 4.9778366E-05 7.7466965E-03 at 50iterations finished qdiffx linear iterations at : 14:14:31 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 4.9778366E-05 7.7466965E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 14:14:32 3.233u 0.182s 0:03.80 89.7% 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 Mon Oct 10 2011 at 14:14:32 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 = 1603 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: 2.168704 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): -6.311000 37.18600 ymin,ymax (A): 1.020000 50.26600 zmin,zma (A): 6.184000 47.56400 x,y,z range (A): 43.49700 49.24600 41.38000 scale (grids/A): 2.168704 object centre (A): 15.43750 25.64300 26.87400 number of atom coordinates read : 1603 total number of charged atoms : 1467 net assigned charge : -7.499990 assigned positive charge : 232.9132 centred at (gu) : 92.00177 94.59362 92.93751 assigned negative charge : -240.4131 centred at (gu) : 92.07594 95.36453 91.95691 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 60276 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14829 grid for indexing accessible points = 1.400000 m= 23954 mr = 40697 m= 4772 mr = 18267 m= 402 mr = 3305 m= 6 mr = 192 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 902 time to turn everything in is 0.4700000 number of dielectric boundary points 26949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 11670 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) : 0.7229014 object centre at (A) : 15.43750 25.64300 26.87400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5837490E-02 2.2499830E-02 midg,1,midg; midg,igrid,midg 3.2294035E-02 -7.4258417E-02 1,midg,midg; igrid,midg,midg -3.8895335E-02 -3.8176857E-02 gauss-seidel spectral radius is 0.9988329 estimated iterations to convergence 232 setup time was (sec) 0.7500000 now iterating at: 14:14:33 rms-change max change #iterations 4.154530 191.6277 at 10iterations 2.050789 76.14200 at 20iterations 1.019177 32.64656 at 30iterations 0.5055221 18.44660 at 40iterations 0.2506739 8.331573 at 50iterations 0.1243175 4.120442 at 60iterations 6.1509464E-02 2.067127 at 70iterations 3.0694857E-02 1.036837 at 80iterations 1.5192068E-02 0.4896088 at 90iterations 7.5249961E-03 0.2326317 at 100iterations 3.7301420E-03 0.1170044 at 110iterations 1.8487058E-03 5.8179855E-02 at 120iterations finished qdiffx linear iterations at : 14:14:39 total time elapsed so far: 7.100000 # loops : 120 mean,max change (kT/e) : 1.8487058E-03 5.8179855E-02 energy calculations done at 7.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.270000 DelPhi exited at 14:14:39 7.270u 0.203s 0:07.80 95.7% 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 Mon Oct 10 2011 at 14:14:40 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 = 1603 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: 3.253056 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): -6.311000 37.18600 ymin,ymax (A): 1.020000 50.26600 zmin,zma (A): 6.184000 47.56400 x,y,z range (A): 43.49700 49.24600 41.38000 scale (grids/A): 3.253056 object centre (A): 15.43750 25.64300 26.87400 number of atom coordinates read : 1603 total number of charged atoms : 1467 net assigned charge : -7.499990 assigned positive charge : 232.9132 centred at (gu) : 93.00282 96.89047 94.40623 assigned negative charge : -240.4131 centred at (gu) : 93.11398 98.04684 92.93545 start vw surface at 0.1500000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 138557 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14829 grid for indexing accessible points = 1.400000 m= 73220 mr = 97775 m= 30949 mr = 60665 m= 9084 mr = 25856 m= 1729 mr = 7285 m= 184 mr = 1262 m= 6 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 2929 time to turn everything in is 1.450000 number of dielectric boundary points 60783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 11736 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) : 2.168704 object centre at (A) : 15.43750 25.64300 26.87400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3746600 0.2741086 midg,1,midg; midg,igrid,midg 0.3812828 -0.6546939 1,midg,midg; igrid,midg,midg -0.2819524 -0.1966489 gauss-seidel spectral radius is 0.9992959 estimated iterations to convergence 297 setup time was (sec) 1.760000 now iterating at: 14:14:42 rms-change max change #iterations 9.125401 325.2152 at 10iterations 5.321738 109.5535 at 20iterations 3.118518 59.21125 at 30iterations 1.815547 39.84917 at 40iterations 1.058352 23.18508 at 50iterations 0.6175489 12.24244 at 60iterations 0.3598331 6.387762 at 70iterations 0.2096943 3.825760 at 80iterations 0.1220206 2.308087 at 90iterations 7.0660003E-02 1.260386 at 100iterations 4.1231181E-02 0.8643156 at 110iterations 2.4055595E-02 0.4497879 at 120iterations 1.3980228E-02 0.2726707 at 130iterations 8.1260949E-03 0.1430244 at 140iterations 4.7218949E-03 9.0816498E-02 at 150iterations 2.7461066E-03 5.2604198E-02 at 160iterations 1.5962202E-03 2.9788971E-02 at 170iterations 9.2980056E-04 1.6340256E-02 at 180iterations finished qdiffx linear iterations at : 14:14:53 total time elapsed so far: 12.57000 # loops : 180 mean,max change (kT/e) : 9.2980056E-04 1.6340256E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 14:14:54 12.749u 0.223s 0:14.28 90.7% 0+0k 0+0io 0pf+0w