Sun Oct 9 12:48:37 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+sph2.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 = amb2.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 Sun Oct 9 2011 at 12:48:37 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 !!! WARNING: GLM 236 has a net charge of -0.0940 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: 0.6772825 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): -5.815000 43.94100 ymin,ymax (A): -14.11300 38.45000 zmin,zma (A): 2.256000 45.07600 x,y,z range (A): 49.75600 52.56300 42.82000 scale (grids/A): 0.6772825 object centre (A): 19.06300 12.16850 23.66600 number of atom coordinates read : 2383 total number of charged atoms : 2238 net assigned charge : 4.406004 assigned positive charge : 366.2110 centred at (gu) : 89.47272 90.54065 90.69322 assigned negative charge : -361.8055 centred at (gu) : 89.42065 90.69913 90.75712 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7331 nv = 96 ne = 84 npr = 47693 no. pairs analyzed = 47693 no. exposed pairs = 3082 no. arc points = 21091 no. surface atoms = 1027 nbur = 1356 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 428 mr = 4017 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 0.2800000 number of dielectric boundary points 3672 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2110 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8497 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1508215E-08 -2.1613471E-10 midg,1,midg; midg,igrid,midg 5.5936610E-08 -3.0913597E-08 1,midg,midg; igrid,midg,midg 3.6207042E-09 2.9600303E-08 gauss-seidel spectral radius is 0.9886764 estimated iterations to convergence 77 setup time was (sec) 0.5200000 now iterating at: 12:48:37 rms-change max change #iterations 0.1783987 28.58052 at 10iterations 2.0662224E-02 3.014093 at 20iterations 3.0937467E-03 0.4574738 at 30iterations 7.8327878E-04 0.1265450 at 40iterations 2.6774342E-04 4.4353485E-02 at 50iterations finished qdiffx linear iterations at : 12:48:40 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 2.6774342E-04 4.4353485E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 12:48:41 3.416u 0.218s 0:03.91 92.5% 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 Sun Oct 9 2011 at 12:48:41 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 !!! WARNING: GLM 236 has a net charge of -0.0940 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: 2.031847 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): -5.815000 43.94100 ymin,ymax (A): -14.11300 38.45000 zmin,zma (A): 2.256000 45.07600 x,y,z range (A): 49.75600 52.56300 42.82000 scale (grids/A): 2.031847 object centre (A): 19.06300 12.16850 23.66600 number of atom coordinates read : 2383 total number of charged atoms : 2238 net assigned charge : 4.406004 assigned positive charge : 366.2110 centred at (gu) : 88.41748 91.62160 92.07908 assigned negative charge : -361.8055 centred at (gu) : 88.26202 92.09684 92.27114 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 78050 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21091 grid for indexing accessible points = 1.400000 m= 29215 mr = 53917 m= 4874 mr = 21408 m= 380 mr = 3052 m= 5 mr = 207 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 33940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17700 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) : 0.6772825 object centre at (A) : 19.06300 12.16850 23.66600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8699128E-02 1.4951010E-02 midg,1,midg; midg,igrid,midg 1.7635191E-02 -5.0403353E-02 1,midg,midg; igrid,midg,midg 2.6473038E-02 8.3477627E-03 gauss-seidel spectral radius is 0.9987759 estimated iterations to convergence 226 setup time was (sec) 0.8400000 now iterating at: 12:48:42 rms-change max change #iterations 4.713521 228.8469 at 10iterations 2.290494 76.40567 at 20iterations 1.117339 38.54269 at 30iterations 0.5439268 16.83796 at 40iterations 0.2655862 7.848520 at 50iterations 0.1294551 4.014658 at 60iterations 6.3418761E-02 1.989920 at 70iterations 3.1203419E-02 0.9407763 at 80iterations 1.5434964E-02 0.4726639 at 90iterations 7.7409032E-03 0.2459564 at 100iterations 4.0018787E-03 0.1235962 at 110iterations 2.1645951E-03 7.3509216E-02 at 120iterations finished qdiffx linear iterations at : 12:48:49 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 2.1645951E-03 7.3509216E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 12:48:49 7.825u 0.290s 0:08.39 96.6% 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 Sun Oct 9 2011 at 12:48:49 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 !!! WARNING: GLM 236 has a net charge of -0.0940 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: 3.047771 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): -5.815000 43.94100 ymin,ymax (A): -14.11300 38.45000 zmin,zma (A): 2.256000 45.07600 x,y,z range (A): 49.75600 52.56300 42.82000 scale (grids/A): 3.047771 object centre (A): 19.06300 12.16850 23.66600 number of atom coordinates read : 2383 total number of charged atoms : 2238 net assigned charge : 4.406004 assigned positive charge : 366.2110 centred at (gu) : 87.62618 92.43224 93.11833 assigned negative charge : -361.8055 centred at (gu) : 87.39297 93.14524 93.40662 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 180467 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21091 grid for indexing accessible points = 1.400000 m= 93525 mr = 130838 m= 34587 mr = 76292 m= 8783 mr = 27527 m= 1696 mr = 6601 m= 143 mr = 1282 m= 2 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.450000 number of dielectric boundary points 76588 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 17900 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) : 2.031847 object centre at (A) : 19.06300 12.16850 23.66600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3798047 7.2546154E-02 midg,1,midg; midg,igrid,midg 0.4462647 -0.7108666 1,midg,midg; igrid,midg,midg 0.2938730 -0.1015410 gauss-seidel spectral radius is 0.9992866 estimated iterations to convergence 295 setup time was (sec) 1.780000 now iterating at: 12:48:51 rms-change max change #iterations 10.65869 387.6957 at 10iterations 6.275572 139.1556 at 20iterations 3.689515 73.46616 at 30iterations 2.165162 43.02203 at 40iterations 1.269100 22.42202 at 50iterations 0.7421882 12.74430 at 60iterations 0.4336222 8.077991 at 70iterations 0.2529017 4.875515 at 80iterations 0.1476711 2.679163 at 90iterations 8.6161345E-02 1.493803 at 100iterations 5.0446060E-02 0.8941574 at 110iterations 2.9656785E-02 0.5769386 at 120iterations 1.7646844E-02 0.3404837 at 130iterations 1.0761209E-02 0.2004547 at 140iterations 6.7717130E-03 0.1442719 at 150iterations 4.4827624E-03 0.1021194 at 160iterations 3.1773453E-03 6.6268921E-02 at 170iterations 2.3899479E-03 5.0956726E-02 at 180iterations finished qdiffx linear iterations at : 12:49:02 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 2.3899479E-03 5.0956726E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.98000 DelPhi exited at 12:49:03 12.987u 0.256s 0:13.51 97.9% 0+0k 0+0io 0pf+0w