Tue Oct 11 06:39:26 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+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 Tue Oct 11 2011 at 06:39:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2029 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: 0.7131124 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): -20.38800 24.73700 ymin,ymax (A): -28.56400 11.19800 zmin,zma (A): -13.32500 36.59700 x,y,z range (A): 45.12500 39.76200 49.92200 scale (grids/A): 0.7131124 object centre (A): 2.174500 -8.683001 11.63600 number of atom coordinates read : 2029 total number of charged atoms : 1901 net assigned charge : 7.500009 assigned positive charge : 306.8221 centred at (gu) : 90.00001 90.46263 89.52551 assigned negative charge : -299.3222 centred at (gu) : 89.82285 90.43327 89.49601 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7031 nv = 96 ne = 84 npr = 40963 no. pairs analyzed = 40963 no. exposed pairs = 2439 no. arc points = 16838 no. surface atoms = 831 nbur = 1198 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 450 mr = 4026 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3385 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1539 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7670 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1601881E-08 8.0669260E-08 midg,1,midg; midg,igrid,midg 5.1954384E-08 9.6185062E-08 1,midg,midg; igrid,midg,midg -2.4606704E-08 1.6601096E-07 gauss-seidel spectral radius is 0.9897430 estimated iterations to convergence 80 setup time was (sec) 0.5400000 now iterating at: 06:39:27 rms-change max change #iterations 0.2005279 31.14153 at 10iterations 2.5335133E-02 3.383595 at 20iterations 3.3522896E-03 0.4777980 at 30iterations 5.0001964E-04 6.4178467E-02 at 40iterations 1.0235808E-04 1.1806488E-02 at 50iterations finished qdiffx linear iterations at : 06:39:31 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 1.0235808E-04 1.1806488E-02 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 06:39:32 4.460u 0.417s 0:05.27 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 Tue Oct 11 2011 at 06:39:32 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 = 2029 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.139337 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): -20.38800 24.73700 ymin,ymax (A): -28.56400 11.19800 zmin,zma (A): -13.32500 36.59700 x,y,z range (A): 45.12500 39.76200 49.92200 scale (grids/A): 2.139337 object centre (A): 2.174500 -8.683001 11.63600 number of atom coordinates read : 2029 total number of charged atoms : 1901 net assigned charge : 7.500009 assigned positive charge : 306.8221 centred at (gu) : 89.99988 91.38798 88.57654 assigned negative charge : -299.3222 centred at (gu) : 89.46858 91.30011 88.48809 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 74389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16838 grid for indexing accessible points = 1.400000 m= 29448 mr = 52846 m= 5807 mr = 22231 m= 563 mr = 3884 m= 15 mr = 276 m= 0 mr = 5 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 30980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 15100 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) : 0.7131124 object centre at (A) : 2.174500 -8.683001 11.63600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2283721E-02 4.6256263E-02 midg,1,midg; midg,igrid,midg 5.8086184E-03 3.7609771E-02 1,midg,midg; igrid,midg,midg 2.2140054E-02 4.1880909E-02 gauss-seidel spectral radius is 0.9988428 estimated iterations to convergence 233 setup time was (sec) 0.9000000 now iterating at: 06:39:33 rms-change max change #iterations 4.575068 222.5322 at 10iterations 2.271175 82.02419 at 20iterations 1.132949 35.62637 at 30iterations 0.5640153 17.21143 at 40iterations 0.2817869 9.914608 at 50iterations 0.1405443 4.261344 at 60iterations 6.9983065E-02 2.205711 at 70iterations 3.4996435E-02 1.159073 at 80iterations 1.7534403E-02 0.5406641 at 90iterations 8.7965541E-03 0.3022532 at 100iterations 4.4135815E-03 0.1297131 at 110iterations 2.2434231E-03 7.5124741E-02 at 120iterations finished qdiffx linear iterations at : 06:39:43 total time elapsed so far: 11.28000 # loops : 120 mean,max change (kT/e) : 2.2434231E-03 7.5124741E-02 energy calculations done at 11.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.45000 DelPhi exited at 06:39:44 11.455u 0.473s 0:12.37 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 Tue Oct 11 2011 at 06:39:44 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 = 2029 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: 3.209006 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): -20.38800 24.73700 ymin,ymax (A): -28.56400 11.19800 zmin,zma (A): -13.32500 36.59700 x,y,z range (A): 45.12500 39.76200 49.92200 scale (grids/A): 3.209006 object centre (A): 2.174500 -8.683001 11.63600 number of atom coordinates read : 2029 total number of charged atoms : 1901 net assigned charge : 7.500009 assigned positive charge : 306.8221 centred at (gu) : 89.99992 92.08201 87.86479 assigned negative charge : -299.3222 centred at (gu) : 89.20295 91.95016 87.73212 start vw surface at 0.1100000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 171517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16838 grid for indexing accessible points = 1.400000 m= 91932 mr = 127234 m= 37450 mr = 76343 m= 11101 mr = 30715 m= 2246 mr = 8647 m= 284 mr = 1604 m= 13 mr = 184 m= 0 mr = 12 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.920000 number of dielectric boundary points 69804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 15208 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) : 2.139337 object centre at (A) : 2.174500 -8.683001 11.63600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6622555 0.3735688 midg,1,midg; midg,igrid,midg 2.4610687E-02 0.2909430 1,midg,midg; igrid,midg,midg 0.3364208 0.3145407 gauss-seidel spectral radius is 0.9992954 estimated iterations to convergence 297 setup time was (sec) 2.240000 now iterating at: 06:39:47 rms-change max change #iterations 10.13523 393.4911 at 10iterations 5.992362 121.8427 at 20iterations 3.538258 76.20934 at 30iterations 2.082427 42.98402 at 40iterations 1.223987 22.13249 at 50iterations 0.7200871 13.05571 at 60iterations 0.4224036 8.022953 at 70iterations 0.2473646 4.624851 at 80iterations 0.1448878 2.521482 at 90iterations 8.4918723E-02 1.458647 at 100iterations 4.9856436E-02 0.9137311 at 110iterations 2.9353399E-02 0.5889530 at 120iterations 1.7387295E-02 0.3152161 at 130iterations 1.0402691E-02 0.1848907 at 140iterations 6.3729533E-03 0.1190767 at 150iterations 4.0288838E-03 7.9933167E-02 at 160iterations 2.6780874E-03 5.1830292E-02 at 170iterations 1.8850553E-03 3.5324097E-02 at 180iterations finished qdiffx linear iterations at : 06:40:02 total time elapsed so far: 17.86000 # loops : 180 mean,max change (kT/e) : 1.8850553E-03 3.5324097E-02 energy calculations done at 17.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.02000 DelPhi exited at 06:40:03 18.029u 0.466s 0:18.81 98.2% 0+0k 0+0io 0pf+0w