Sun Oct 9 19:03:57 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 Sun Oct 9 2011 at 19:03:57 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5191 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5500959 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): 3.272000 67.98800 ymin,ymax (A): -9.076000 53.29500 zmin,zma (A): -2.573000 61.51900 x,y,z range (A): 64.71600 62.37100 64.09200 scale (grids/A): 0.5500959 object centre (A): 35.63000 22.10950 29.47300 number of atom coordinates read : 5191 total number of charged atoms : 5045 net assigned charge : -0.3789439 assigned positive charge : 796.9894 centred at (gu) : 87.84481 89.33244 89.80306 assigned negative charge : -797.3746 centred at (gu) : 87.72524 89.36797 89.76286 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 10194 nv = 96 ne = 84 npr = 105684 no. pairs analyzed = 105684 no. exposed pairs = 5963 no. arc points = 40904 no. surface atoms = 2041 nbur = 3150 mkacc time = 0.2500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 457 mr = 5845 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4775 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4192 ## 465 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 13478 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7395089E-10 5.3545351E-10 midg,1,midg; midg,igrid,midg 5.9013106E-10 -4.0787138E-10 1,midg,midg; igrid,midg,midg -2.8720253E-09 9.6070274E-10 gauss-seidel spectral radius is 0.9831178 estimated iterations to convergence 63 setup time was (sec) 0.7600000 now iterating at: 19:03:58 rms-change max change #iterations 0.1063511 12.89528 at 10iterations 9.4553391E-03 1.376930 at 20iterations 2.5650773E-03 0.3051910 at 30iterations 1.1222376E-03 0.1359344 at 40iterations 5.1317021E-04 6.5664768E-02 at 50iterations finished qdiffx linear iterations at : 19:04:01 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 5.1317021E-04 6.5664768E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 19:04:01 3.613u 0.140s 0:04.04 92.8% 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 19:04:01 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5191 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.650288 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): 3.272000 67.98800 ymin,ymax (A): -9.076000 53.29500 zmin,zma (A): -2.573000 61.51900 x,y,z range (A): 64.71600 62.37100 64.09200 scale (grids/A): 1.650288 object centre (A): 35.63000 22.10950 29.47300 number of atom coordinates read : 5191 total number of charged atoms : 5045 net assigned charge : -0.3789439 assigned positive charge : 796.9894 centred at (gu) : 83.53303 87.99576 89.40744 assigned negative charge : -797.3746 centred at (gu) : 83.17572 88.10388 89.28880 start vw surface at 0.2300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 114039 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40904 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 38749 mr = 82835 m= 4482 mr = 28111 m= 142 mr = 2397 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 44051 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 406 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 38712 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) : 0.5500959 object centre at (A) : 35.63000 22.10950 29.47300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9464472E-02 -1.4857603E-02 midg,1,midg; midg,igrid,midg 2.0772062E-02 7.5235930E-03 1,midg,midg; igrid,midg,midg -2.6830498E-02 1.5925752E-02 gauss-seidel spectral radius is 0.9984211 estimated iterations to convergence 200 setup time was (sec) 1.110000 now iterating at: 19:04:02 rms-change max change #iterations 4.822548 172.6715 at 10iterations 2.132021 65.13693 at 20iterations 0.9461193 27.36562 at 30iterations 0.4195714 12.33818 at 40iterations 0.1864741 5.111412 at 50iterations 8.2959980E-02 2.314980 at 60iterations 3.7146147E-02 1.098982 at 70iterations 1.6917374E-02 0.4499903 at 80iterations 8.0735805E-03 0.2230072 at 90iterations 4.1882596E-03 0.1116961 at 100iterations 2.4755227E-03 7.1754932E-02 at 110iterations 1.6583385E-03 4.4859886E-02 at 120iterations finished qdiffx linear iterations at : 19:04:09 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.6583385E-03 4.4859886E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 19:04:10 7.938u 0.154s 0:08.37 96.5% 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 19:04:10 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5191 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.475431 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): 3.272000 67.98800 ymin,ymax (A): -9.076000 53.29500 zmin,zma (A): -2.573000 61.51900 x,y,z range (A): 64.71600 62.37100 64.09200 scale (grids/A): 2.475431 object centre (A): 35.63000 22.10950 29.47300 number of atom coordinates read : 5191 total number of charged atoms : 5045 net assigned charge : -0.3789439 assigned positive charge : 796.9894 centred at (gu) : 80.29906 86.99353 89.11092 assigned negative charge : -797.3746 centred at (gu) : 79.76340 87.15562 88.93319 start vw surface at 0.2100000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 265208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40904 grid for indexing accessible points = 1.400000 m= 132132 mr = 201541 m= 40736 mr = 107921 m= 7324 mr = 31708 m= 652 mr = 5043 m= 14 mr = 318 m= 0 mr = 4 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.980000 number of dielectric boundary points 99531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 40307 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) : 1.650288 object centre at (A) : 35.63000 22.10950 29.47300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3135599 -0.3355194 midg,1,midg; midg,igrid,midg 0.1363253 -5.6213196E-02 1,midg,midg; igrid,midg,midg -0.4692154 0.2281814 gauss-seidel spectral radius is 0.9992503 estimated iterations to convergence 288 setup time was (sec) 2.290000 now iterating at: 19:04:12 rms-change max change #iterations 12.27956 341.9509 at 10iterations 7.240281 152.9254 at 20iterations 4.241572 76.19427 at 30iterations 2.472179 45.88243 at 40iterations 1.435605 27.05847 at 50iterations 0.8329408 14.82584 at 60iterations 0.4807678 8.824249 at 70iterations 0.2777354 4.616259 at 80iterations 0.1603865 2.675255 at 90iterations 9.2491344E-02 1.523087 at 100iterations 5.3249277E-02 0.8204498 at 110iterations 3.0826002E-02 0.5034599 at 120iterations 1.7959358E-02 0.3264990 at 130iterations 1.0605664E-02 0.1859684 at 140iterations 6.4363182E-03 0.1229172 at 150iterations 4.0869145E-03 7.7255249E-02 at 160iterations 2.7634667E-03 5.5540562E-02 at 170iterations 2.0035079E-03 3.7166595E-02 at 180iterations finished qdiffx linear iterations at : 19:04:24 total time elapsed so far: 13.76000 # loops : 180 mean,max change (kT/e) : 2.0035079E-03 3.7166595E-02 energy calculations done at 13.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.94000 DelPhi exited at 19:04:24 13.943u 0.197s 0:14.41 98.0% 0+0k 0+0io 0pf+0w