Sat Oct 15 12:55:40 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 Sat Oct 15 2011 at 12:55:40 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 = 2433 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: 0.6920685 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): -6.332000 43.64200 ymin,ymax (A): -13.67100 37.76900 zmin,zma (A): 2.164000 44.70000 x,y,z range (A): 49.97400 51.43999 42.53600 scale (grids/A): 0.6920685 object centre (A): 18.65500 12.04900 23.43200 number of atom coordinates read : 2433 total number of charged atoms : 2291 net assigned charge : 5.500019 assigned positive charge : 372.8199 centred at (gu) : 89.65057 91.00088 91.05727 assigned negative charge : -367.3205 centred at (gu) : 89.61610 91.14756 91.15636 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7712 nv = 96 ne = 84 npr = 49523 no. pairs analyzed = 49523 no. exposed pairs = 2919 no. arc points = 20184 no. surface atoms = 998 nbur = 1435 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 439 mr = 4312 m= 5 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.1900000 number of dielectric boundary points 3748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1915 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8956 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9550445E-08 -1.0076082E-08 midg,1,midg; midg,igrid,midg 7.5718930E-08 -3.4442746E-08 1,midg,midg; igrid,midg,midg 2.0353994E-08 4.4162263E-08 gauss-seidel spectral radius is 0.9891535 estimated iterations to convergence 78 setup time was (sec) 0.3900000 now iterating at: 12:55:40 rms-change max change #iterations 0.1961097 28.16549 at 10iterations 2.3880219E-02 3.249078 at 20iterations 3.4377428E-03 0.5140915 at 30iterations 8.0148061E-04 0.1208420 at 40iterations 2.6254644E-04 3.6342621E-02 at 50iterations finished qdiffx linear iterations at : 12:55:43 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 2.6254644E-04 3.6342621E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 12:55:44 3.490u 0.195s 0:04.09 89.9% 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 Sat Oct 15 2011 at 12:55:44 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 = 2433 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: 2.076205 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): -6.332000 43.64200 ymin,ymax (A): -13.67100 37.76900 zmin,zma (A): 2.164000 44.70000 x,y,z range (A): 49.97400 51.43999 42.53600 scale (grids/A): 2.076205 object centre (A): 18.65500 12.04900 23.43200 number of atom coordinates read : 2433 total number of charged atoms : 2291 net assigned charge : 5.500019 assigned positive charge : 372.8199 centred at (gu) : 88.95096 93.00182 93.17137 assigned negative charge : -367.3205 centred at (gu) : 88.84818 93.44247 93.46885 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 82615 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20184 grid for indexing accessible points = 1.400000 m= 31586 mr = 58258 m= 5727 mr = 23823 m= 496 mr = 3688 m= 17 mr = 251 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 34419 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 18181 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) : 0.6920685 object centre at (A) : 18.65500 12.04900 23.43200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6895785E-02 1.1613796E-02 midg,1,midg; midg,igrid,midg 3.7945352E-02 -2.6701553E-02 1,midg,midg; igrid,midg,midg 5.0778836E-02 3.3458138E-03 gauss-seidel spectral radius is 0.9988198 estimated iterations to convergence 230 setup time was (sec) 0.6400000 now iterating at: 12:55:45 rms-change max change #iterations 4.870059 219.4470 at 10iterations 2.390476 96.58151 at 20iterations 1.186812 39.46334 at 30iterations 0.5866089 18.65472 at 40iterations 0.2900213 8.892450 at 50iterations 0.1434978 4.369105 at 60iterations 7.1006179E-02 2.045713 at 70iterations 3.5443999E-02 1.024626 at 80iterations 1.7694497E-02 0.5274000 at 90iterations 8.9489305E-03 0.2849331 at 100iterations 4.5913043E-03 0.1348276 at 110iterations 2.4810019E-03 8.2611084E-02 at 120iterations finished qdiffx linear iterations at : 12:55:52 total time elapsed so far: 8.140000 # loops : 120 mean,max change (kT/e) : 2.4810019E-03 8.2611084E-02 energy calculations done at 8.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.270000 DelPhi exited at 12:55:53 8.272u 0.226s 0:08.89 95.5% 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 15 2011 at 12:55:53 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 = 2433 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: 3.114308 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): -6.332000 43.64200 ymin,ymax (A): -13.67100 37.76900 zmin,zma (A): 2.164000 44.70000 x,y,z range (A): 49.97400 51.43999 42.53600 scale (grids/A): 3.114308 object centre (A): 18.65500 12.04900 23.43200 number of atom coordinates read : 2433 total number of charged atoms : 2291 net assigned charge : 5.500019 assigned positive charge : 372.8199 centred at (gu) : 88.42641 94.50255 94.75703 assigned negative charge : -367.3205 centred at (gu) : 88.27235 95.16367 95.20323 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 190999 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20184 grid for indexing accessible points = 1.400000 m= 100216 mr = 140968 m= 38791 mr = 83034 m= 10643 mr = 31652 m= 2089 mr = 8180 m= 244 mr = 1510 m= 17 mr = 165 m= 0 mr = 2 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 77488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 18328 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) : 2.076205 object centre at (A) : 18.65500 12.04900 23.43200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5360959 2.8215614E-03 midg,1,midg; midg,igrid,midg 0.7251981 -0.2947628 1,midg,midg; igrid,midg,midg 0.5785678 -0.1583598 gauss-seidel spectral radius is 0.9992949 estimated iterations to convergence 297 setup time was (sec) 1.530000 now iterating at: 12:55:54 rms-change max change #iterations 10.98620 374.7150 at 10iterations 6.497276 132.3798 at 20iterations 3.832326 79.49919 at 30iterations 2.259691 40.81910 at 40iterations 1.328310 26.44355 at 50iterations 0.7804069 14.76542 at 60iterations 0.4580650 7.559863 at 70iterations 0.2681169 4.514081 at 80iterations 0.1567709 2.576287 at 90iterations 9.2091016E-02 1.524208 at 100iterations 5.4083209E-02 0.9145260 at 110iterations 3.1806704E-02 0.5176544 at 120iterations 1.8946469E-02 0.3023605 at 130iterations 1.1448205E-02 0.2113495 at 140iterations 7.1389326E-03 0.1302643 at 150iterations 4.6741567E-03 9.5222473E-02 at 160iterations 3.2440652E-03 7.9975128E-02 at 170iterations 2.4016837E-03 5.1330566E-02 at 180iterations finished qdiffx linear iterations at : 12:56:07 total time elapsed so far: 13.50000 # loops : 180 mean,max change (kT/e) : 2.4016837E-03 5.1330566E-02 energy calculations done at 13.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.63000 DelPhi exited at 12:56:07 13.634u 0.243s 0:14.55 95.3% 0+0k 0+0io 0pf+0w