Mon Oct 10 09:10:11 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 09:10:11 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6325628 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): -35.13500 10.44200 ymin,ymax (A): 1.597000 42.40600 zmin,zma (A): -0.1940000 56.08500 x,y,z range (A): 45.57700 40.80900 56.27900 scale (grids/A): 0.6325628 object centre (A): -12.34650 22.00150 27.94550 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 3.000004 assigned positive charge : 290.6719 centred at (gu) : 90.27504 89.08896 89.97372 assigned negative charge : -287.6722 centred at (gu) : 90.20023 89.22835 89.97244 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5346 nv = 96 ne = 84 npr = 40514 no. pairs analyzed = 40514 no. exposed pairs = 2420 no. arc points = 16861 no. surface atoms = 824 nbur = 1144 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 314 mr = 3024 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1667 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6384 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3378216E-09 3.4809475E-09 midg,1,midg; midg,igrid,midg 1.5960158E-08 -5.3398850E-09 1,midg,midg; igrid,midg,midg -1.7802633E-09 9.1647205E-09 gauss-seidel spectral radius is 0.9869986 estimated iterations to convergence 72 setup time was (sec) 0.3500000 now iterating at: 09:10:12 rms-change max change #iterations 0.1187959 18.47174 at 10iterations 1.1561197E-02 2.058281 at 20iterations 1.0990767E-03 0.1821117 at 30iterations 1.0628964E-04 1.7609596E-02 at 40iterations 9.9884974E-06 1.5411377E-03 at 50iterations finished qdiffx linear iterations at : 09:10:14 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 9.9884974E-06 1.5411377E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 09:10:15 3.351u 0.177s 0:04.02 87.5% 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 Mon Oct 10 2011 at 09:10:15 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.897688 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): -35.13500 10.44200 ymin,ymax (A): 1.597000 42.40600 zmin,zma (A): -0.1940000 56.08500 x,y,z range (A): 45.57700 40.80900 56.27900 scale (grids/A): 1.897688 object centre (A): -12.34650 22.00150 27.94550 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 3.000004 assigned positive charge : 290.6719 centred at (gu) : 90.82510 87.26694 89.92110 assigned negative charge : -287.6722 centred at (gu) : 90.60111 87.68506 89.91751 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 57346 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16861 grid for indexing accessible points = 1.400000 m= 21799 mr = 39735 m= 3607 mr = 16757 m= 212 mr = 2485 m= 1 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 104 time to turn everything in is 0.3000000 number of dielectric boundary points 23912 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 14449 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) : 0.6325628 object centre at (A) : -12.34650 22.00150 27.94550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6601821E-02 3.4628481E-02 midg,1,midg; midg,igrid,midg 2.3430332E-03 -7.0666950E-03 1,midg,midg; igrid,midg,midg -4.3461695E-03 -4.0270211E-03 gauss-seidel spectral radius is 0.9985498 estimated iterations to convergence 208 setup time was (sec) 0.5200000 now iterating at: 09:10:16 rms-change max change #iterations 3.551569 181.2672 at 10iterations 1.626395 58.58524 at 20iterations 0.7472562 26.19464 at 30iterations 0.3418390 12.57210 at 40iterations 0.1564585 5.215626 at 50iterations 7.1357369E-02 2.413743 at 60iterations 3.2649737E-02 1.157238 at 70iterations 1.4996893E-02 0.5500779 at 80iterations 6.8326686E-03 0.2367134 at 90iterations 3.1234056E-03 0.1189804 at 100iterations 1.4340782E-03 4.7472596E-02 at 110iterations 6.5670616E-04 2.2274017E-02 at 120iterations finished qdiffx linear iterations at : 09:10:23 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 6.5670616E-04 2.2274017E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 09:10:23 7.672u 0.206s 0:08.18 96.2% 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 09:10:23 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.846532 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): -35.13500 10.44200 ymin,ymax (A): 1.597000 42.40600 zmin,zma (A): -0.1940000 56.08500 x,y,z range (A): 45.57700 40.80900 56.27900 scale (grids/A): 2.846532 object centre (A): -12.34650 22.00150 27.94550 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 3.000004 assigned positive charge : 290.6719 centred at (gu) : 91.23755 85.90038 89.88174 assigned negative charge : -287.6722 centred at (gu) : 90.90157 86.52768 89.87628 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 132098 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16861 grid for indexing accessible points = 1.400000 m= 69160 mr = 95586 m= 26760 mr = 57813 m= 6710 mr = 22422 m= 924 mr = 5308 m= 71 mr = 647 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 350 time to turn everything in is 0.7500000 number of dielectric boundary points 53908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 14687 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) : 1.897688 object centre at (A) : -12.34650 22.00150 27.94550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8455177E-02 0.2239753 midg,1,midg; midg,igrid,midg -6.2477909E-02 -0.1007698 1,midg,midg; igrid,midg,midg -8.5537471E-02 -7.9500109E-02 gauss-seidel spectral radius is 0.9992189 estimated iterations to convergence 282 setup time was (sec) 0.9800000 now iterating at: 09:10:24 rms-change max change #iterations 8.336860 391.8480 at 10iterations 4.747743 108.4723 at 20iterations 2.677148 53.94988 at 30iterations 1.517394 34.10794 at 40iterations 0.8540906 16.83818 at 50iterations 0.4840063 11.35287 at 60iterations 0.2725804 6.367731 at 70iterations 0.1539959 2.930459 at 80iterations 8.7043777E-02 1.646256 at 90iterations 4.9156025E-02 1.056850 at 100iterations 2.7780356E-02 0.5660095 at 110iterations 1.5719334E-02 0.3376455 at 120iterations 8.8608926E-03 0.1871471 at 130iterations 4.9906941E-03 0.1031055 at 140iterations 2.8210995E-03 5.9703827E-02 at 150iterations 1.5953378E-03 3.2404184E-02 at 160iterations 9.0035528E-04 1.6796112E-02 at 170iterations 5.0894800E-04 9.8285675E-03 at 180iterations finished qdiffx linear iterations at : 09:10:36 total time elapsed so far: 12.02000 # loops : 180 mean,max change (kT/e) : 5.0894800E-04 9.8285675E-03 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.15000 DelPhi exited at 09:10:36 12.154u 0.213s 0:12.68 97.4% 0+0k 0+0io 0pf+0w