Mon Oct 10 14:01:15 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 Mon Oct 10 2011 at 14:01:15 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2724 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 0.5726788 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): -20.79700 41.36700 ymin,ymax (A): -12.62900 44.53300 zmin,zma (A): -1.779000 52.49800 x,y,z range (A): 62.16399 57.16200 54.27700 scale (grids/A): 0.5726788 object centre (A): 10.28500 15.95200 25.35950 number of atom coordinates read : 2724 total number of charged atoms : 2578 net assigned charge : 11.01402 assigned positive charge : 401.4801 centred at (gu) : 91.69070 91.11914 86.61840 assigned negative charge : -390.4666 centred at (gu) : 91.82401 91.19512 86.37616 start vw surface at 0.2200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6018 nv = 96 ne = 84 npr = 52713 no. pairs analyzed = 52713 no. exposed pairs = 4074 no. arc points = 29873 no. surface atoms = 1359 nbur = 1365 mkacc time = 0.1200000 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 = 1.484000 m= 298 mr = 2611 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2939 ## 348 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0139310E-09 2.5069316E-09 midg,1,midg; midg,igrid,midg 2.4138964E-09 1.1301845E-09 1,midg,midg; igrid,midg,midg 2.6685134E-09 -3.0655763E-11 gauss-seidel spectral radius is 0.9842628 estimated iterations to convergence 66 setup time was (sec) 0.6100000 now iterating at: 14:01:15 rms-change max change #iterations 8.9432120E-02 14.51640 at 10iterations 6.6823573E-03 1.214941 at 20iterations 5.0788332E-04 7.9144478E-02 at 30iterations 4.6850360E-05 6.3323975E-03 at 40iterations 6.7074425E-06 7.4291229E-04 at 50iterations finished qdiffx linear iterations at : 14:01:18 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 6.7074425E-06 7.4291229E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 14:01:19 3.433u 0.202s 0:04.03 90.0% 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 Mon Oct 10 2011 at 14:01:19 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2724 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 1.718036 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): -20.79700 41.36700 ymin,ymax (A): -12.62900 44.53300 zmin,zma (A): -1.779000 52.49800 x,y,z range (A): 62.16399 57.16200 54.27700 scale (grids/A): 1.718036 object centre (A): 10.28500 15.95200 25.35950 number of atom coordinates read : 2724 total number of charged atoms : 2578 net assigned charge : 11.01402 assigned positive charge : 401.4801 centred at (gu) : 95.07186 93.35718 79.85484 assigned negative charge : -390.4666 centred at (gu) : 95.47194 93.58516 79.12839 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 65008 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29873 grid for indexing accessible points = 1.400000 m= 19896 mr = 39467 m= 2355 mr = 12515 m= 92 mr = 975 m= 0 mr = 7 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.4800000 number of dielectric boundary points 34387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 289 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19958 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) : 0.5726788 object centre at (A) : 10.28500 15.95200 25.35950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4611278E-03 1.3570022E-02 midg,1,midg; midg,igrid,midg 2.4006095E-02 2.2324182E-02 1,midg,midg; igrid,midg,midg 1.0929313E-02 -1.5784718E-02 gauss-seidel spectral radius is 0.9983538 estimated iterations to convergence 196 setup time was (sec) 0.7600000 now iterating at: 14:01:20 rms-change max change #iterations 3.454046 165.9155 at 10iterations 1.483767 58.53467 at 20iterations 0.6457239 23.64056 at 30iterations 0.2783199 10.36076 at 40iterations 0.1199614 4.346825 at 50iterations 5.2124698E-02 1.750164 at 60iterations 2.2543935E-02 0.8436279 at 70iterations 9.7699342E-03 0.3438568 at 80iterations 4.2390805E-03 0.1560040 at 90iterations 1.8309822E-03 7.9394341E-02 at 100iterations 7.9811050E-04 2.9588699E-02 at 110iterations 3.4693506E-04 1.4289856E-02 at 120iterations finished qdiffx linear iterations at : 14:01:26 total time elapsed so far: 7.040000 # loops : 120 mean,max change (kT/e) : 3.4693506E-04 1.4289856E-02 energy calculations done at 7.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.240000 DelPhi exited at 14:01:27 7.238u 0.148s 0:08.24 89.4% 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 14:01:27 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2724 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 2.577055 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): -20.79700 41.36700 ymin,ymax (A): -12.62900 44.53300 zmin,zma (A): -1.779000 52.49800 x,y,z range (A): 62.16399 57.16200 54.27700 scale (grids/A): 2.577055 object centre (A): 10.28500 15.95200 25.35950 number of atom coordinates read : 2724 total number of charged atoms : 2578 net assigned charge : 11.01402 assigned positive charge : 401.4801 centred at (gu) : 97.60773 95.03557 74.78209 assigned negative charge : -390.4666 centred at (gu) : 98.20778 95.37773 73.69260 start vw surface at 0.1400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 150562 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29873 grid for indexing accessible points = 1.400000 m= 66557 mr = 97765 m= 20364 mr = 49533 m= 3616 mr = 14198 m= 317 mr = 2111 m= 2 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 1.100000 number of dielectric boundary points 77700 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 20614 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) : 1.718036 object centre at (A) : 10.28500 15.95200 25.35950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5744885E-02 0.1430920 midg,1,midg; midg,igrid,midg 0.4364841 0.2586184 1,midg,midg; igrid,midg,midg 0.1902485 -0.4150879 gauss-seidel spectral radius is 0.9991942 estimated iterations to convergence 278 setup time was (sec) 1.400000 now iterating at: 14:01:29 rms-change max change #iterations 9.006373 296.7479 at 10iterations 5.286102 151.9295 at 20iterations 3.069932 84.21770 at 30iterations 1.760427 46.15685 at 40iterations 1.003582 29.01228 at 50iterations 0.5712569 14.91462 at 60iterations 0.3235969 7.835724 at 70iterations 0.1832301 5.002671 at 80iterations 0.1034326 2.444887 at 90iterations 5.8212485E-02 1.352217 at 100iterations 3.2892715E-02 0.7419300 at 110iterations 1.8483007E-02 0.4384110 at 120iterations 1.0368290E-02 0.2331333 at 130iterations 5.8288076E-03 0.1240501 at 140iterations 3.2677203E-03 6.9297791E-02 at 150iterations 1.8315634E-03 4.0435791E-02 at 160iterations 1.0298569E-03 2.1054864E-02 at 170iterations 5.7899626E-04 1.3664246E-02 at 180iterations finished qdiffx linear iterations at : 14:01:39 total time elapsed so far: 11.22000 # loops : 180 mean,max change (kT/e) : 5.7899626E-04 1.3664246E-02 energy calculations done at 11.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.39000 DelPhi exited at 14:01:39 11.395u 0.233s 0:11.97 97.0% 0+0k 0+0io 0pf+0w