Wed Dec 21 14:21:34 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+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 Wed Dec 21 2011 at 14:21:36 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 0.6567175 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): -5.818000 35.15700 ymin,ymax (A): -3.204000 50.57300 zmin,zma (A): -23.19200 31.01700 x,y,z range (A): 40.97500 53.77700 54.20900 scale (grids/A): 0.6567175 object centre (A): 14.66950 23.68450 3.912500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 291.4260 centred at (gu) : 90.84579 92.23419 89.83512 assigned negative charge : -287.4263 centred at (gu) : 90.92736 92.33073 89.78879 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5932 nv = 96 ne = 84 npr = 39946 no. pairs analyzed = 39946 no. exposed pairs = 2377 no. arc points = 17091 no. surface atoms = 812 nbur = 1150 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 325 mr = 3379 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.1800000 number of dielectric boundary points 2822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1696 ## 169 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 6720 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5757721E-09 1.5332880E-08 midg,1,midg; midg,igrid,midg 1.4199601E-08 -5.8366827E-09 1,midg,midg; igrid,midg,midg 1.7219431E-08 -1.6788023E-09 gauss-seidel spectral radius is 0.9879277 estimated iterations to convergence 74 setup time was (sec) 0.5200000 now iterating at: 14:21:37 rms-change max change #iterations 0.1412031 19.27728 at 10iterations 1.4946409E-02 2.200756 at 20iterations 1.5280433E-03 0.2443924 at 30iterations 1.5987399E-04 2.4467945E-02 at 40iterations 1.7267193E-05 2.5386810E-03 at 50iterations finished qdiffx linear iterations at : 14:21:42 total time elapsed so far: 5.100000 # loops : 50 mean,max change (kT/e) : 1.7267193E-05 2.5386810E-03 energy calculations done at 5.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.240000 DelPhi exited at 14:21:50 5.241u 0.409s 0:15.68 35.9% 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 21 2011 at 14:22:03 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 1.970153 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): -5.818000 35.15700 ymin,ymax (A): -3.204000 50.57300 zmin,zma (A): -23.19200 31.01700 x,y,z range (A): 40.97500 53.77700 54.20900 scale (grids/A): 1.970153 object centre (A): 14.66950 23.68450 3.912500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 291.4260 centred at (gu) : 92.53743 96.70249 89.50536 assigned negative charge : -287.4263 centred at (gu) : 92.78227 96.99239 89.36656 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 62841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17091 grid for indexing accessible points = 1.400000 m= 25188 mr = 43827 m= 4524 mr = 19735 m= 313 mr = 3116 m= 3 mr = 156 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1389 time to turn everything in is 0.3600000 number of dielectric boundary points 26035 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 14496 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) : 0.6567175 object centre at (A) : 14.66950 23.68450 3.912500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4603001E-02 1.5014459E-02 midg,1,midg; midg,igrid,midg 3.9874505E-02 1.7469786E-03 1,midg,midg; igrid,midg,midg 8.9546898E-03 -3.4161948E-03 gauss-seidel spectral radius is 0.9986458 estimated iterations to convergence 215 setup time was (sec) 0.5800000 now iterating at: 14:22:04 rms-change max change #iterations 3.849919 219.4515 at 10iterations 1.810332 66.91246 at 20iterations 0.8516249 30.86564 at 30iterations 0.3982352 13.68628 at 40iterations 0.1879475 6.428413 at 50iterations 8.8041618E-02 3.115319 at 60iterations 4.1217271E-02 1.287088 at 70iterations 1.9406961E-02 0.6497955 at 80iterations 9.1171619E-03 0.3054483 at 90iterations 4.2754784E-03 0.1492920 at 100iterations 2.0075729E-03 7.7322006E-02 at 110iterations 9.4548363E-04 3.5367012E-02 at 120iterations finished qdiffx linear iterations at : 14:22:13 total time elapsed so far: 9.010000 # loops : 120 mean,max change (kT/e) : 9.4548363E-04 3.5367012E-02 energy calculations done at 9.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.150000 DelPhi exited at 14:22:27 9.149u 0.241s 0:25.24 37.1% 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 21 2011 at 14:22:30 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 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: 2.955229 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): -5.818000 35.15700 ymin,ymax (A): -3.204000 50.57300 zmin,zma (A): -23.19200 31.01700 x,y,z range (A): 40.97500 53.77700 54.20900 scale (grids/A): 2.955229 object centre (A): 14.66950 23.68450 3.912500 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 4.000003 assigned positive charge : 291.4260 centred at (gu) : 93.80599 100.0536 89.25799 assigned negative charge : -287.4263 centred at (gu) : 94.17353 100.4886 89.04987 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 144830 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17091 grid for indexing accessible points = 1.400000 m= 78277 mr = 105270 m= 32087 mr = 65905 m= 8232 mr = 27304 m= 1341 mr = 6601 m= 105 mr = 967 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 4618 time to turn everything in is 0.8700000 number of dielectric boundary points 58757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 14639 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) : 1.970153 object centre at (A) : 14.66950 23.68450 3.912500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8840883 4.8692308E-02 midg,1,midg; midg,igrid,midg 0.3504122 -7.5414225E-02 1,midg,midg; igrid,midg,midg 4.8632734E-02 -2.0024503E-02 gauss-seidel spectral radius is 0.9992492 estimated iterations to convergence 288 setup time was (sec) 1.140000 now iterating at: 14:22:32 rms-change max change #iterations 8.968076 412.2943 at 10iterations 5.184244 136.6217 at 20iterations 2.972888 70.39960 at 30iterations 1.708635 35.89767 at 40iterations 0.9827508 19.51200 at 50iterations 0.5607756 11.18960 at 60iterations 0.3213296 6.377687 at 70iterations 0.1836949 3.986327 at 80iterations 0.1051057 2.319825 at 90iterations 6.0121167E-02 1.364464 at 100iterations 3.4278750E-02 0.6770153 at 110iterations 1.9637391E-02 0.3748957 at 120iterations 1.1211062E-02 0.2479858 at 130iterations 6.4014331E-03 0.1218176 at 140iterations 3.6503254E-03 7.0632935E-02 at 150iterations 2.0893509E-03 4.5452595E-02 at 160iterations 1.1944387E-03 2.3567200E-02 at 170iterations 6.8249210E-04 1.2316465E-02 at 180iterations finished qdiffx linear iterations at : 14:22:48 total time elapsed so far: 16.88000 # loops : 180 mean,max change (kT/e) : 6.8249210E-04 1.2316465E-02 energy calculations done at 16.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.02000 DelPhi exited at 14:22:59 17.023u 0.310s 0:30.07 57.6% 0+0k 0+0io 0pf+0w