Wed Dec 28 11:02:20 PST 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 Wed Dec 28 2011 at 11:02:21 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6020632 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): -8.849000 50.28100 ymin,ymax (A): 8.693001 51.78400 zmin,zma (A): -4.016000 38.87800 x,y,z range (A): 59.13000 43.09100 42.89400 scale (grids/A): 0.6020632 object centre (A): 20.71600 30.23850 17.43100 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 4.000004 assigned positive charge : 286.9561 centred at (gu) : 90.18572 89.02760 90.49114 assigned negative charge : -282.9563 centred at (gu) : 90.16565 88.91266 90.66084 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4809 nv = 96 ne = 84 npr = 39677 no. pairs analyzed = 39677 no. exposed pairs = 2441 no. arc points = 17113 no. surface atoms = 827 nbur = 1131 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 246 mr = 2663 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2600000 number of dielectric boundary points 2383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1697 ## 169 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 5802 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9151235E-09 -3.3763017E-09 midg,1,midg; midg,igrid,midg -1.7818094E-09 4.1066359E-09 1,midg,midg; igrid,midg,midg 1.2767435E-09 2.5692319E-09 gauss-seidel spectral radius is 0.9856675 estimated iterations to convergence 68 setup time was (sec) 0.7500000 now iterating at: 11:02:22 rms-change max change #iterations 9.5362216E-02 14.04939 at 10iterations 7.9745883E-03 1.314627 at 20iterations 6.8132399E-04 0.1215019 at 30iterations 5.6856923E-05 9.8648071E-03 at 40iterations 4.8532838E-06 7.8201294E-04 at 50iterations finished qdiffx linear iterations at : 11:02:27 total time elapsed so far: 5.490000 # loops : 50 mean,max change (kT/e) : 4.8532838E-06 7.8201294E-04 energy calculations done at 5.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.670000 DelPhi exited at 11:02:28 5.672u 0.728s 0:07.01 91.1% 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 Wed Dec 28 2011 at 11:02:28 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.806190 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): -8.849000 50.28100 ymin,ymax (A): 8.693001 51.78400 zmin,zma (A): -4.016000 38.87800 x,y,z range (A): 59.13000 43.09100 42.89400 scale (grids/A): 1.806190 object centre (A): 20.71600 30.23850 17.43100 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 4.000004 assigned positive charge : 286.9561 centred at (gu) : 90.55743 87.08285 91.47368 assigned negative charge : -282.9563 centred at (gu) : 90.49727 86.73816 91.98267 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 52334 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17113 grid for indexing accessible points = 1.400000 m= 18263 mr = 36021 m= 2298 mr = 13603 m= 68 mr = 1365 m= 0 mr = 9 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 233 time to turn everything in is 0.5000000 number of dielectric boundary points 21965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 14280 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) : 0.6020632 object centre at (A) : 20.71600 30.23850 17.43100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1007183E-03 -3.5742987E-03 midg,1,midg; midg,igrid,midg 2.0345724E-03 7.3975064E-03 1,midg,midg; igrid,midg,midg 2.7691673E-02 4.2594291E-02 gauss-seidel spectral radius is 0.9984085 estimated iterations to convergence 199 setup time was (sec) 1.030000 now iterating at: 11:02:30 rms-change max change #iterations 3.163423 157.8681 at 10iterations 1.393000 61.72525 at 20iterations 0.6152706 25.97409 at 30iterations 0.2710777 10.29294 at 40iterations 0.1192751 4.461025 at 50iterations 5.2611593E-02 2.119843 at 60iterations 2.3170024E-02 0.8375244 at 70iterations 1.0161064E-02 0.3910904 at 80iterations 4.4928514E-03 0.1793132 at 90iterations 1.9800100E-03 8.2832336E-02 at 100iterations 8.7245728E-04 3.1665802E-02 at 110iterations 3.8321482E-04 1.4724731E-02 at 120iterations finished qdiffx linear iterations at : 11:02:47 total time elapsed so far: 17.81000 # loops : 120 mean,max change (kT/e) : 3.8321482E-04 1.4724731E-02 energy calculations done at 17.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.97000 DelPhi exited at 11:02:48 17.977u 0.811s 0:19.70 95.3% 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 Wed Dec 28 2011 at 11:02:48 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.709285 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): -8.849000 50.28100 ymin,ymax (A): 8.693001 51.78400 zmin,zma (A): -4.016000 38.87800 x,y,z range (A): 59.13000 43.09100 42.89400 scale (grids/A): 2.709285 object centre (A): 20.71600 30.23850 17.43100 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 4.000004 assigned positive charge : 286.9561 centred at (gu) : 90.83617 85.62428 92.21056 assigned negative charge : -282.9563 centred at (gu) : 90.74587 85.10725 92.97408 start vw surface at 0.1100000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 121219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17113 grid for indexing accessible points = 1.400000 m= 60435 mr = 87108 m= 20236 mr = 49947 m= 3804 mr = 16493 m= 295 mr = 2820 m= 6 mr = 157 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 778 time to turn everything in is 1.300000 number of dielectric boundary points 49470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 14608 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) : 1.806190 object centre at (A) : 20.71600 30.23850 17.43100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8490826E-02 -9.8887105E-03 midg,1,midg; midg,igrid,midg 8.8712290E-02 5.8032170E-02 1,midg,midg; igrid,midg,midg 0.3030646 0.5822253 gauss-seidel spectral radius is 0.9991782 estimated iterations to convergence 275 setup time was (sec) 1.890000 now iterating at: 11:02:50 rms-change max change #iterations 7.720587 326.2916 at 10iterations 4.367447 122.0784 at 20iterations 2.451030 59.10583 at 30iterations 1.374561 33.69314 at 40iterations 0.7673120 18.68863 at 50iterations 0.4283806 9.994040 at 60iterations 0.2389792 5.721397 at 70iterations 0.1327309 2.976568 at 80iterations 7.3946103E-02 1.585483 at 90iterations 4.1223079E-02 0.9721985 at 100iterations 2.2968812E-02 0.5851116 at 110iterations 1.2816031E-02 0.3064863 at 120iterations 7.1067596E-03 0.1549625 at 130iterations 3.9603594E-03 8.2530975E-02 at 140iterations 2.2064343E-03 5.0571442E-02 at 150iterations 1.2272761E-03 2.4706364E-02 at 160iterations 6.8049773E-04 1.6872406E-02 at 170iterations 3.8031494E-04 8.5906982E-03 at 180iterations finished qdiffx linear iterations at : 11:03:19 total time elapsed so far: 30.05000 # loops : 180 mean,max change (kT/e) : 3.8031494E-04 8.5906982E-03 energy calculations done at 30.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.22000 DelPhi exited at 11:03:19 30.226u 0.878s 0:31.43 98.9% 0+0k 0+0io 0pf+0w