Mon Oct 10 09:13:30 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 09:13:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6449276 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): -6.504000 34.37600 ymin,ymax (A): -3.466000 48.13300 zmin,zma (A): -24.22800 30.97200 x,y,z range (A): 40.88000 51.59900 55.20000 scale (grids/A): 0.6449276 object centre (A): 13.93600 22.33350 3.372001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 91.02881 92.50105 90.13575 assigned negative charge : -284.8263 centred at (gu) : 91.14086 92.63065 90.09212 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5495 nv = 96 ne = 84 npr = 41002 no. pairs analyzed = 41002 no. exposed pairs = 2426 no. arc points = 16898 no. surface atoms = 818 nbur = 1146 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 294 mr = 3085 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.1700000 number of dielectric boundary points 2677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1672 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6531 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1991299E-09 9.9646771E-09 midg,1,midg; midg,igrid,midg 1.0559226E-08 -1.2864222E-08 1,midg,midg; igrid,midg,midg 1.3032253E-08 -6.9824928E-09 gauss-seidel spectral radius is 0.9874841 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 09:13:30 rms-change max change #iterations 0.1314163 22.46434 at 10iterations 1.3168349E-02 2.372448 at 20iterations 1.3364546E-03 0.2059193 at 30iterations 1.3312227E-04 2.6054382E-02 at 40iterations 1.3303052E-05 2.4108887E-03 at 50iterations finished qdiffx linear iterations at : 09:13:33 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.3303052E-05 2.4108887E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 09:13:34 3.347u 0.202s 0:03.90 90.7% 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 09:13:34 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 = 1964 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: 1.934783 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): -6.504000 34.37600 ymin,ymax (A): -3.466000 48.13300 zmin,zma (A): -24.22800 30.97200 x,y,z range (A): 40.88000 51.59900 55.20000 scale (grids/A): 1.934783 object centre (A): 13.93600 22.33350 3.372001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 93.08658 97.50343 90.40731 assigned negative charge : -284.8263 centred at (gu) : 93.42281 97.89202 90.27650 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 59054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16898 grid for indexing accessible points = 1.400000 m= 21679 mr = 40969 m= 3537 mr = 16530 m= 207 mr = 2312 m= 3 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 2458 time to turn everything in is 0.3100000 number of dielectric boundary points 24585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 14454 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) : 0.6449276 object centre at (A) : 13.93600 22.33350 3.372001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0551534E-02 1.7687889E-02 midg,1,midg; midg,igrid,midg 3.6328450E-02 -6.0207061E-03 1,midg,midg; igrid,midg,midg 8.0557959E-03 -7.3427600E-03 gauss-seidel spectral radius is 0.9985952 estimated iterations to convergence 211 setup time was (sec) 0.5300000 now iterating at: 09:13:34 rms-change max change #iterations 3.666043 181.0984 at 10iterations 1.702430 68.67563 at 20iterations 0.7901009 32.47326 at 30iterations 0.3660816 12.89448 at 40iterations 0.1696881 6.352844 at 50iterations 7.8003481E-02 2.941548 at 60iterations 3.6296282E-02 1.257451 at 70iterations 1.6845858E-02 0.5768337 at 80iterations 7.7591538E-03 0.2974224 at 90iterations 3.5978609E-03 0.1309128 at 100iterations 1.6644947E-03 5.6541443E-02 at 110iterations 7.7264325E-04 2.4475098E-02 at 120iterations finished qdiffx linear iterations at : 09:13:41 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 7.7264325E-04 2.4475098E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 09:13:42 7.755u 0.195s 0:08.20 96.8% 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 09:13:42 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 = 1964 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: 2.902174 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): -6.504000 34.37600 ymin,ymax (A): -3.466000 48.13300 zmin,zma (A): -24.22800 30.97200 x,y,z range (A): 40.88000 51.59900 55.20000 scale (grids/A): 2.902174 object centre (A): 13.93600 22.33350 3.372001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 94.62983 101.2551 90.61111 assigned negative charge : -284.8263 centred at (gu) : 95.13427 101.8381 90.41489 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 136184 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16898 grid for indexing accessible points = 1.400000 m= 69790 mr = 98627 m= 26235 mr = 58117 m= 6384 mr = 21754 m= 929 mr = 4940 m= 53 mr = 654 m= 0 mr = 20 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 7861 time to turn everything in is 0.7900000 number of dielectric boundary points 55463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 14655 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) : 1.934783 object centre at (A) : 13.93600 22.33350 3.372001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.072729 2.5961895E-02 midg,1,midg; midg,igrid,midg 0.3600115 -8.7470159E-02 1,midg,midg; igrid,midg,midg 4.7983363E-02 -5.3497169E-02 gauss-seidel spectral radius is 0.9992341 estimated iterations to convergence 285 setup time was (sec) 1.020000 now iterating at: 09:13:43 rms-change max change #iterations 8.562823 351.0483 at 10iterations 4.927151 112.2807 at 20iterations 2.812090 70.46313 at 30iterations 1.597166 42.28600 at 40iterations 0.9114189 22.55184 at 50iterations 0.5179589 12.71444 at 60iterations 0.2946766 6.527553 at 70iterations 0.1673433 3.463745 at 80iterations 9.5198691E-02 1.981218 at 90iterations 5.4029878E-02 1.328602 at 100iterations 3.0636542E-02 0.6031647 at 110iterations 1.7415280E-02 0.3226869 at 120iterations 9.8917438E-03 0.1796541 at 130iterations 5.6114201E-03 0.1144886 at 140iterations 3.1882790E-03 6.2763214E-02 at 150iterations 1.8086727E-03 3.7401199E-02 at 160iterations 1.0270814E-03 2.1232605E-02 at 170iterations 5.8464840E-04 1.1482239E-02 at 180iterations finished qdiffx linear iterations at : 09:13:54 total time elapsed so far: 11.97000 # loops : 180 mean,max change (kT/e) : 5.8464840E-04 1.1482239E-02 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.10000 DelPhi exited at 09:13:55 12.102u 0.206s 0:12.62 97.4% 0+0k 0+0io 0pf+0w