Mon Oct 10 14:01:29 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 Mon Oct 10 2011 at 14:01:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 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: 0.6750735 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): -14.33400 38.40100 ymin,ymax (A): 0.3790001 44.61300 zmin,zma (A): -7.211000 43.79800 x,y,z range (A): 52.73500 44.23400 51.00900 scale (grids/A): 0.6750735 object centre (A): 12.03350 22.49600 18.29350 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500024 assigned positive charge : 370.2130 centred at (gu) : 90.59802 91.06657 90.26273 assigned negative charge : -366.7136 centred at (gu) : 90.79330 91.13152 90.22872 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7194 nv = 96 ne = 84 npr = 48426 no. pairs analyzed = 48426 no. exposed pairs = 3126 no. arc points = 21113 no. surface atoms = 1049 nbur = 1367 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 477 mr = 3885 m= 6 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3710 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1953 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8467 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3518726E-09 2.4332920E-08 midg,1,midg; midg,igrid,midg 2.5329832E-08 -5.1608380E-09 1,midg,midg; igrid,midg,midg 5.8347734E-08 -4.5915211E-08 gauss-seidel spectral radius is 0.9886039 estimated iterations to convergence 76 setup time was (sec) 0.3900000 now iterating at: 14:01:30 rms-change max change #iterations 0.1802776 27.18852 at 10iterations 2.0455565E-02 3.117878 at 20iterations 2.6931199E-03 0.4270344 at 30iterations 5.6084752E-04 9.1583252E-02 at 40iterations 1.7572442E-04 2.8869629E-02 at 50iterations finished qdiffx linear iterations at : 14:01:33 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.7572442E-04 2.8869629E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 14:01:33 3.368u 0.147s 0:04.15 84.3% 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 Mon Oct 10 2011 at 14:01:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 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: 2.025221 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): -14.33400 38.40100 ymin,ymax (A): 0.3790001 44.61300 zmin,zma (A): -7.211000 43.79800 x,y,z range (A): 52.73500 44.23400 51.00900 scale (grids/A): 2.025221 object centre (A): 12.03350 22.49600 18.29350 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500024 assigned positive charge : 370.2130 centred at (gu) : 91.79352 93.19910 90.78741 assigned negative charge : -366.7136 centred at (gu) : 92.37952 93.39429 90.68591 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76899 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21113 grid for indexing accessible points = 1.400000 m= 29847 mr = 53007 m= 5421 mr = 21894 m= 400 mr = 3456 m= 11 mr = 173 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 281 time to turn everything in is 0.3800000 number of dielectric boundary points 34048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17994 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) : 0.6750735 object centre at (A) : 12.03350 22.49600 18.29350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1063024E-02 2.0996992E-02 midg,1,midg; midg,igrid,midg 3.1919468E-02 3.4886599E-03 1,midg,midg; igrid,midg,midg 2.3537135E-02 -5.7641707E-02 gauss-seidel spectral radius is 0.9987687 estimated iterations to convergence 226 setup time was (sec) 0.6000000 now iterating at: 14:01:34 rms-change max change #iterations 4.650008 210.5923 at 10iterations 2.254085 74.01959 at 20iterations 1.099217 34.17158 at 30iterations 0.5345965 17.09293 at 40iterations 0.2605334 7.693308 at 50iterations 0.1271028 3.796860 at 60iterations 6.2063511E-02 1.862228 at 70iterations 3.0358307E-02 0.9060059 at 80iterations 1.4885538E-02 0.4822636 at 90iterations 7.3988969E-03 0.2188435 at 100iterations 3.7578212E-03 0.1351852 at 110iterations 1.9557900E-03 5.9568405E-02 at 120iterations finished qdiffx linear iterations at : 14:01:41 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 1.9557900E-03 5.9568405E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 14:01:42 7.700u 0.190s 0:08.68 90.8% 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 Mon Oct 10 2011 at 14:01:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 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: 3.037831 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): -14.33400 38.40100 ymin,ymax (A): 0.3790001 44.61300 zmin,zma (A): -7.211000 43.79800 x,y,z range (A): 52.73500 44.23400 51.00900 scale (grids/A): 3.037831 object centre (A): 12.03350 22.49600 18.29350 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500024 assigned positive charge : 370.2130 centred at (gu) : 92.69013 94.79870 91.18104 assigned negative charge : -366.7136 centred at (gu) : 93.56912 95.09143 91.02885 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 177433 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21113 grid for indexing accessible points = 1.400000 m= 92923 mr = 128312 m= 37151 mr = 75634 m= 10092 mr = 29854 m= 1776 mr = 7582 m= 208 mr = 1190 m= 6 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 905 time to turn everything in is 1.030000 number of dielectric boundary points 76889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 18192 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) : 2.025221 object centre at (A) : 12.03350 22.49600 18.29350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3180034 0.1972944 midg,1,midg; midg,igrid,midg 0.3088496 -8.0228209E-02 1,midg,midg; igrid,midg,midg 0.4038219 -0.6258726 gauss-seidel spectral radius is 0.9992872 estimated iterations to convergence 296 setup time was (sec) 1.260000 now iterating at: 14:01:44 rms-change max change #iterations 10.70736 444.9279 at 10iterations 6.351499 134.0926 at 20iterations 3.754541 73.37585 at 30iterations 2.210209 43.99077 at 40iterations 1.300052 24.01999 at 50iterations 0.7620318 13.85081 at 60iterations 0.4479165 7.855919 at 70iterations 0.2607843 5.100592 at 80iterations 0.1526988 2.955817 at 90iterations 8.9456342E-02 1.616623 at 100iterations 5.2307140E-02 0.8842506 at 110iterations 3.0720353E-02 0.5877686 at 120iterations 1.8101627E-02 0.3409542 at 130iterations 1.0831187E-02 0.2014313 at 140iterations 6.6210367E-03 0.1466637 at 150iterations 4.2090178E-03 9.0286255E-02 at 160iterations 2.8032803E-03 6.1820984E-02 at 170iterations 1.9797280E-03 4.6180725E-02 at 180iterations finished qdiffx linear iterations at : 14:01:55 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 1.9797280E-03 4.6180725E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 14:01:56 12.535u 0.202s 0:13.50 94.2% 0+0k 0+0io 0pf+0w