Mon Oct 10 13:58:08 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 13:58:08 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7353093 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): 8.486000 56.90100 ymin,ymax (A): -8.906000 36.93600 zmin,zma (A): -3.026000 43.96400 x,y,z range (A): 48.41500 45.84200 46.99000 scale (grids/A): 0.7353093 object centre (A): 32.69350 14.01500 20.46900 number of atom coordinates read : 2118 total number of charged atoms : 1979 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 89.39326 90.40602 89.96523 assigned negative charge : -323.3720 centred at (gu) : 89.43775 90.51270 90.18441 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8011 nv = 96 ne = 84 npr = 43444 no. pairs analyzed = 43444 no. exposed pairs = 2670 no. arc points = 18744 no. surface atoms = 901 nbur = 1217 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 587 mr = 4525 m= 2 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 111 time to turn everything in is 0.2800000 number of dielectric boundary points 3911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1608 ## 127 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8425 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0138198E-07 -3.0605230E-07 midg,1,midg; midg,igrid,midg -1.3311742E-09 -2.1567381E-07 1,midg,midg; igrid,midg,midg -6.4526681E-08 -1.2612919E-07 gauss-seidel spectral radius is 0.9903641 estimated iterations to convergence 83 setup time was (sec) 0.5400000 now iterating at: 13:58:09 rms-change max change #iterations 0.2460189 36.20709 at 10iterations 3.2195829E-02 3.638596 at 20iterations 4.3350514E-03 0.5189314 at 30iterations 5.8006623E-04 7.3125839E-02 at 40iterations 7.7431920E-05 1.1135101E-02 at 50iterations finished qdiffx linear iterations at : 13:58:12 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 7.7431920E-05 1.1135101E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 13:58:12 3.504u 0.170s 0:03.99 91.9% 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 13:58:12 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.205928 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): 8.486000 56.90100 ymin,ymax (A): -8.906000 36.93600 zmin,zma (A): -3.026000 43.96400 x,y,z range (A): 48.41500 45.84200 46.99000 scale (grids/A): 2.205928 object centre (A): 32.69350 14.01500 20.46900 number of atom coordinates read : 2118 total number of charged atoms : 1979 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 88.17991 91.21778 89.89565 assigned negative charge : -323.3720 centred at (gu) : 88.31332 91.53792 90.55325 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83093 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18744 grid for indexing accessible points = 1.400000 m= 34904 mr = 57649 m= 8192 mr = 27018 m= 993 mr = 5923 m= 41 mr = 611 m= 0 mr = 12 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 2872 time to turn everything in is 0.6500000 number of dielectric boundary points 36010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15761 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) : 0.7353093 object centre at (A) : 32.69350 14.01500 20.46900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1184781E-02 -0.1305807 midg,1,midg; midg,igrid,midg -2.4412429E-02 -4.0484585E-02 1,midg,midg; igrid,midg,midg 6.2319371E-03 -9.1681238E-03 gauss-seidel spectral radius is 0.9989139 estimated iterations to convergence 240 setup time was (sec) 0.9600000 now iterating at: 13:58:14 rms-change max change #iterations 5.049996 185.0658 at 10iterations 2.540704 71.44534 at 20iterations 1.293407 43.73667 at 30iterations 0.6555487 19.18869 at 40iterations 0.3330002 10.05844 at 50iterations 0.1693042 5.018486 at 60iterations 8.5946463E-02 2.417213 at 70iterations 4.3690961E-02 1.377547 at 80iterations 2.2155074E-02 0.6413713 at 90iterations 1.1305174E-02 0.3177252 at 100iterations 5.7258015E-03 0.1695976 at 110iterations 2.9104853E-03 8.9893341E-02 at 120iterations finished qdiffx linear iterations at : 13:58:21 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 2.9104853E-03 8.9893341E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.110000 DelPhi exited at 13:58:21 8.113u 0.203s 0:08.79 94.5% 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 Mon Oct 10 2011 at 13:58:21 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.308892 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): 8.486000 56.90100 ymin,ymax (A): -8.906000 36.93600 zmin,zma (A): -3.026000 43.96400 x,y,z range (A): 48.41500 45.84200 46.99000 scale (grids/A): 3.308892 object centre (A): 32.69350 14.01500 20.46900 number of atom coordinates read : 2118 total number of charged atoms : 1979 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 87.26982 91.82667 89.84361 assigned negative charge : -323.3720 centred at (gu) : 87.46992 92.30701 90.82993 start vw surface at 0.1500000 fill in re-entrant regions at 0.9400000 boundary points on vw surface= 191035 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18744 grid for indexing accessible points = 1.400000 m= 104726 mr = 138724 m= 47962 mr = 87496 m= 16153 mr = 40417 m= 3937 mr = 13178 m= 611 mr = 3126 m= 31 mr = 455 m= 0 mr = 13 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 9666 time to turn everything in is 2.130000 number of dielectric boundary points 81046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.280000 number of grid points assigned charge 15832 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) : 2.205928 object centre at (A) : 32.69350 14.01500 20.46900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7670005E-02 -1.342039 midg,1,midg; midg,igrid,midg -0.2180382 -0.1929848 1,midg,midg; igrid,midg,midg 1.8961197E-02 -8.3831824E-02 gauss-seidel spectral radius is 0.9993137 estimated iterations to convergence 301 setup time was (sec) 2.460000 now iterating at: 13:58:24 rms-change max change #iterations 10.86171 315.8559 at 10iterations 6.371953 109.7941 at 20iterations 3.747947 82.74704 at 30iterations 2.200210 39.60631 at 40iterations 1.288447 21.92152 at 50iterations 0.7551063 11.76743 at 60iterations 0.4428092 7.768206 at 70iterations 0.2595600 3.997756 at 80iterations 0.1522907 2.473688 at 90iterations 8.9214064E-02 1.512045 at 100iterations 5.2225463E-02 0.7782555 at 110iterations 3.0576462E-02 0.4789200 at 120iterations 1.7914940E-02 0.3027196 at 130iterations 1.0518230E-02 0.1703606 at 140iterations 6.1656279E-03 0.1033111 at 150iterations 3.6073620E-03 5.6819916E-02 at 160iterations 2.1190732E-03 3.4086108E-02 at 170iterations 1.2425117E-03 2.0570002E-02 at 180iterations finished qdiffx linear iterations at : 13:58:35 total time elapsed so far: 13.52000 # loops : 180 mean,max change (kT/e) : 1.2425117E-03 2.0570002E-02 energy calculations done at 13.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.71000 DelPhi exited at 13:58:36 13.711u 0.226s 0:14.29 97.4% 0+0k 0+0io 0pf+0w