Tue Nov 22 14:12:46 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 Tue Nov 22 2011 at 14:12:50 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: 274 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: 0.6432611 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): -6.316000 34.94700 ymin,ymax (A): -3.660000 50.00600 zmin,zma (A): -24.38700 30.95600 x,y,z range (A): 41.26300 53.66600 55.34300 scale (grids/A): 0.6432611 object centre (A): 14.31550 23.17300 3.284501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 90.95213 92.15611 90.24508 assigned negative charge : -288.8263 centred at (gu) : 91.05618 92.28606 90.18454 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5599 nv = 96 ne = 84 npr = 40146 no. pairs analyzed = 40146 no. exposed pairs = 2411 no. arc points = 17062 no. surface atoms = 816 nbur = 1148 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 305 mr = 3174 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2100000 number of dielectric boundary points 2696 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1694 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6489 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2829285E-10 1.1409472E-08 midg,1,midg; midg,igrid,midg 1.0932236E-08 -1.1852563E-08 1,midg,midg; igrid,midg,midg 1.2138758E-08 -5.9076894E-09 gauss-seidel spectral radius is 0.9874229 estimated iterations to convergence 73 setup time was (sec) 0.4500000 now iterating at: 14:12:54 rms-change max change #iterations 0.1316243 22.22701 at 10iterations 1.2982891E-02 2.013916 at 20iterations 1.2901672E-03 0.2146368 at 30iterations 1.2947814E-04 1.8276215E-02 at 40iterations 1.2868212E-05 2.1824837E-03 at 50iterations finished qdiffx linear iterations at : 14:12:59 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 1.2868212E-05 2.1824837E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 14:13:04 3.137u 0.153s 0:15.05 21.7% 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 Tue Nov 22 2011 at 14:13:07 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: 274 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: 1.929783 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): -6.316000 34.94700 ymin,ymax (A): -3.660000 50.00600 zmin,zma (A): -24.38700 30.95600 x,y,z range (A): 41.26300 53.66600 55.34300 scale (grids/A): 1.929783 object centre (A): 14.31550 23.17300 3.284501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 92.85649 96.46839 90.73517 assigned negative charge : -288.8263 centred at (gu) : 93.16875 96.85831 90.55383 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 59877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17062 grid for indexing accessible points = 1.400000 m= 22112 mr = 41508 m= 3401 mr = 16988 m= 181 mr = 2199 m= 7 mr = 61 m= 0 mr = 4 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2696 time to turn everything in is 0.4300000 number of dielectric boundary points 24818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 14453 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) : 0.6432611 object centre at (A) : 14.31550 23.17300 3.284501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9962802E-02 1.7708711E-02 midg,1,midg; midg,igrid,midg 3.6370095E-02 -1.1269689E-02 1,midg,midg; igrid,midg,midg 9.7361924E-03 -3.1246385E-03 gauss-seidel spectral radius is 0.9985915 estimated iterations to convergence 211 setup time was (sec) 0.7100000 now iterating at: 14:13:12 rms-change max change #iterations 3.708646 169.8042 at 10iterations 1.721357 78.02544 at 20iterations 0.7983536 29.94348 at 30iterations 0.3701624 13.90016 at 40iterations 0.1711658 5.835808 at 50iterations 7.8746945E-02 2.746942 at 60iterations 3.6462907E-02 1.234959 at 70iterations 1.6873758E-02 0.5727806 at 80iterations 7.7906051E-03 0.2813993 at 90iterations 3.6246425E-03 0.1283588 at 100iterations 1.6781334E-03 6.0069799E-02 at 110iterations 7.7680679E-04 2.9537201E-02 at 120iterations finished qdiffx linear iterations at : 14:13:32 total time elapsed so far: 7.340000 # loops : 120 mean,max change (kT/e) : 7.7680679E-04 2.9537201E-02 energy calculations done at 7.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 14:13:36 7.520u 0.194s 0:29.01 26.5% 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 Tue Nov 22 2011 at 14:13:37 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: 274 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: 2.894675 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): -6.316000 34.94700 ymin,ymax (A): -3.660000 50.00600 zmin,zma (A): -24.38700 30.95600 x,y,z range (A): 41.26300 53.66600 55.34300 scale (grids/A): 2.894675 object centre (A): 14.31550 23.17300 3.284501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 94.28466 99.70255 91.10271 assigned negative charge : -288.8263 centred at (gu) : 94.75320 100.2875 90.83076 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 138521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17062 grid for indexing accessible points = 1.400000 m= 71292 mr = 100502 m= 26275 mr = 59397 m= 5985 mr = 21811 m= 770 mr = 4650 m= 48 mr = 508 m= 5 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.5999999 no. cavity mid-points inaccessible to solvent = 8933 time to turn everything in is 1.080000 number of dielectric boundary points 55996 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 14656 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) : 1.929783 object centre at (A) : 14.31550 23.17300 3.284501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9903326 4.1206848E-02 midg,1,midg; midg,igrid,midg 0.3762580 -0.1524707 1,midg,midg; igrid,midg,midg 6.1502486E-02 -9.3997493E-03 gauss-seidel spectral radius is 0.9992318 estimated iterations to convergence 285 setup time was (sec) 1.390000 now iterating at: 14:13:42 rms-change max change #iterations 8.609089 308.7826 at 10iterations 4.905257 126.7446 at 20iterations 2.776069 57.14354 at 30iterations 1.574544 32.25469 at 40iterations 0.8971617 17.96799 at 50iterations 0.5076773 10.01816 at 60iterations 0.2877164 6.064705 at 70iterations 0.1634499 3.066774 at 80iterations 9.2578486E-02 1.866951 at 90iterations 5.2593254E-02 0.9870434 at 100iterations 2.9821800E-02 0.6038237 at 110iterations 1.6922185E-02 0.3613453 at 120iterations 9.5769493E-03 0.2293091 at 130iterations 5.4284208E-03 0.1053624 at 140iterations 3.0816039E-03 6.1705589E-02 at 150iterations 1.7521473E-03 3.7788391E-02 at 160iterations 9.9206052E-04 2.0751953E-02 at 170iterations 5.6311529E-04 1.1085987E-02 at 180iterations finished qdiffx linear iterations at : 14:14:04 total time elapsed so far: 11.56000 # loops : 180 mean,max change (kT/e) : 5.6311529E-04 1.1085987E-02 energy calculations done at 11.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.74000 DelPhi exited at 14:14:11 11.744u 0.209s 0:33.90 35.2% 0+0k 0+0io 0pf+0w