Tue Oct 11 00:58:31 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 00:58:31 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 = 2784 !!! WARNING: LEU 299 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6409333 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): -15.56100 34.80000 ymin,ymax (A): -25.84400 27.22900 zmin,zma (A): -22.77500 32.76900 x,y,z range (A): 50.36100 53.07300 55.54400 scale (grids/A): 0.6409333 object centre (A): 9.619501 0.6925001 4.997001 number of atom coordinates read : 2784 total number of charged atoms : 2638 net assigned charge : 4.228017 assigned positive charge : 420.9974 centred at (gu) : 88.77195 89.16479 89.63788 assigned negative charge : -416.7701 centred at (gu) : 88.71101 89.19303 89.86648 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7590 nv = 96 ne = 84 npr = 56603 no. pairs analyzed = 56603 no. exposed pairs = 3245 no. arc points = 23188 no. surface atoms = 1101 nbur = 1683 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 395 mr = 4273 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 112 time to turn everything in is 0.3300000 number of dielectric boundary points 3649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2321 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9210 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7736196E-08 -2.1923910E-08 midg,1,midg; midg,igrid,midg 1.1828798E-08 2.2796676E-09 1,midg,midg; igrid,midg,midg -2.1681854E-09 1.0852531E-08 gauss-seidel spectral radius is 0.9874017 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 00:58:32 rms-change max change #iterations 0.1546958 23.88319 at 10iterations 1.5810862E-02 2.205547 at 20iterations 1.9562596E-03 0.3307533 at 30iterations 3.8049606E-04 8.3171844E-02 at 40iterations 1.0117125E-04 2.3517609E-02 at 50iterations finished qdiffx linear iterations at : 00:58:35 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.0117125E-04 2.3517609E-02 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 00:58:36 3.567u 0.190s 0:04.36 86.0% 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 00:58:36 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 = 2784 !!! WARNING: LEU 299 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.922800 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): -15.56100 34.80000 ymin,ymax (A): -25.84400 27.22900 zmin,zma (A): -22.77500 32.76900 x,y,z range (A): 50.36100 53.07300 55.54400 scale (grids/A): 1.922800 object centre (A): 9.619501 0.6925001 4.997001 number of atom coordinates read : 2784 total number of charged atoms : 2638 net assigned charge : 4.228017 assigned positive charge : 420.9974 centred at (gu) : 86.31496 87.49361 88.91277 assigned negative charge : -416.7701 centred at (gu) : 86.13271 87.57885 89.59897 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 82049 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23188 grid for indexing accessible points = 1.400000 m= 29442 mr = 57487 m= 4655 mr = 22154 m= 257 mr = 3027 m= 2 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 4438 time to turn everything in is 0.6200000 number of dielectric boundary points 33633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20777 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) : 0.6409333 object centre at (A) : 9.619501 0.6925001 4.997001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9414539E-02 -3.8231734E-02 midg,1,midg; midg,igrid,midg 1.8809021E-03 1.7648678E-02 1,midg,midg; igrid,midg,midg 1.3775556E-02 1.0537294E-02 gauss-seidel spectral radius is 0.9986714 estimated iterations to convergence 217 setup time was (sec) 0.9300000 now iterating at: 00:58:37 rms-change max change #iterations 4.519287 162.2965 at 10iterations 2.132296 70.48114 at 20iterations 1.009214 35.92865 at 30iterations 0.4776521 15.01297 at 40iterations 0.2257884 6.897331 at 50iterations 0.1067576 3.089318 at 60iterations 5.0724160E-02 1.850761 at 70iterations 2.4128577E-02 0.6847143 at 80iterations 1.1477585E-02 0.3576241 at 90iterations 5.5017592E-03 0.1797628 at 100iterations 2.6766167E-03 7.8727722E-02 at 110iterations 1.3312596E-03 5.0907135E-02 at 120iterations finished qdiffx linear iterations at : 00:58:44 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 1.3312596E-03 5.0907135E-02 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 00:58:45 8.173u 0.231s 0:08.94 93.9% 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 Tue Oct 11 2011 at 00:58:45 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 = 2784 !!! WARNING: LEU 299 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: 2.884200 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): -15.56100 34.80000 ymin,ymax (A): -25.84400 27.22900 zmin,zma (A): -22.77500 32.76900 x,y,z range (A): 50.36100 53.07300 55.54400 scale (grids/A): 2.884200 object centre (A): 9.619501 0.6925001 4.997001 number of atom coordinates read : 2784 total number of charged atoms : 2638 net assigned charge : 4.228017 assigned positive charge : 420.9974 centred at (gu) : 84.47249 86.24038 88.36912 assigned negative charge : -416.7701 centred at (gu) : 84.19895 86.36822 89.39841 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 189482 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23188 grid for indexing accessible points = 1.400000 m= 95770 mr = 139016 m= 34869 mr = 79198 m= 8526 mr = 28498 m= 1209 mr = 6559 m= 59 mr = 824 m= 0 mr = 21 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 14794 time to turn everything in is 1.560000 number of dielectric boundary points 75799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 21104 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) : 1.922800 object centre at (A) : 9.619501 0.6925001 4.997001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9253021 -0.3581122 midg,1,midg; midg,igrid,midg -3.4209348E-02 0.1234350 1,midg,midg; igrid,midg,midg 0.3840678 0.1040080 gauss-seidel spectral radius is 0.9992623 estimated iterations to convergence 291 setup time was (sec) 1.890000 now iterating at: 00:58:47 rms-change max change #iterations 10.40618 440.2760 at 10iterations 6.044973 154.3421 at 20iterations 3.500674 83.44592 at 30iterations 2.024994 35.14075 at 40iterations 1.166584 19.89819 at 50iterations 0.6726615 11.66205 at 60iterations 0.3869792 6.701395 at 70iterations 0.2229460 3.887751 at 80iterations 0.1281691 2.333678 at 90iterations 7.3951162E-02 1.262707 at 100iterations 4.2517360E-02 0.7582207 at 110iterations 2.4504444E-02 0.4333668 at 120iterations 1.4132175E-02 0.2454395 at 130iterations 8.1940508E-03 0.1397552 at 140iterations 4.7632130E-03 8.1846237E-02 at 150iterations 2.8098756E-03 5.9967995E-02 at 160iterations 1.6854707E-03 3.4271240E-02 at 170iterations 1.0464430E-03 2.2357941E-02 at 180iterations finished qdiffx linear iterations at : 00:58:58 total time elapsed so far: 13.06000 # loops : 180 mean,max change (kT/e) : 1.0464430E-03 2.2357941E-02 energy calculations done at 13.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.25000 DelPhi exited at 00:58:58 13.249u 0.249s 0:13.83 97.4% 0+0k 0+0io 0pf+0w