Tue Oct 11 08:21:05 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 Tue Oct 11 2011 at 08:21:05 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2104 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6877499 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): -16.31300 29.00000 ymin,ymax (A): -11.48700 36.45300 zmin,zma (A): 0.2650000 52.02800 x,y,z range (A): 45.31300 47.94000 51.76300 scale (grids/A): 0.6877499 object centre (A): 6.343500 12.48300 26.14650 number of atom coordinates read : 2104 total number of charged atoms : 2005 net assigned charge : 2.000009 assigned positive charge : 316.1715 centred at (gu) : 90.43983 89.98870 89.48981 assigned negative charge : -314.1719 centred at (gu) : 90.47138 90.01749 89.21960 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6917 nv = 96 ne = 84 npr = 42433 no. pairs analyzed = 42433 no. exposed pairs = 2793 no. arc points = 19773 no. surface atoms = 938 nbur = 1166 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 454 mr = 3789 m= 4 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3000000 number of dielectric boundary points 3538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1852 ## 141 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7872 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5483023E-08 8.5141771E-08 midg,1,midg; midg,igrid,midg 2.0265567E-08 1.9780615E-09 1,midg,midg; igrid,midg,midg 1.9328112E-08 1.1444811E-09 gauss-seidel spectral radius is 0.9889982 estimated iterations to convergence 78 setup time was (sec) 0.5800000 now iterating at: 08:21:06 rms-change max change #iterations 0.1788764 27.65965 at 10iterations 2.0561069E-02 2.857951 at 20iterations 2.3915812E-03 0.3116875 at 30iterations 2.9712016E-04 3.9762497E-02 at 40iterations 4.2736723E-05 6.3915253E-03 at 50iterations finished qdiffx linear iterations at : 08:21:09 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 4.2736723E-05 6.3915253E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 08:21:10 4.023u 0.255s 0:04.70 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 Tue Oct 11 2011 at 08:21:10 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2104 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.063250 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): -16.31300 29.00000 ymin,ymax (A): -11.48700 36.45300 zmin,zma (A): 0.2650000 52.02800 x,y,z range (A): 45.31300 47.94000 51.76300 scale (grids/A): 2.063250 object centre (A): 6.343500 12.48300 26.14650 number of atom coordinates read : 2104 total number of charged atoms : 2005 net assigned charge : 2.000009 assigned positive charge : 316.1715 centred at (gu) : 91.31918 89.96593 88.46923 assigned negative charge : -314.1719 centred at (gu) : 91.41417 90.05238 87.65882 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 74069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19773 grid for indexing accessible points = 1.400000 m= 27295 mr = 50838 m= 4833 mr = 20042 m= 317 mr = 2961 m= 9 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 470 time to turn everything in is 0.6700000 number of dielectric boundary points 32596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15921 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) : 0.6877499 object centre at (A) : 6.343500 12.48300 26.14650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0975557E-02 7.0735961E-02 midg,1,midg; midg,igrid,midg 1.0348490E-02 -3.0683914E-02 1,midg,midg; igrid,midg,midg 1.3108850E-02 -1.0053329E-02 gauss-seidel spectral radius is 0.9987885 estimated iterations to convergence 227 setup time was (sec) 0.9600000 now iterating at: 08:21:11 rms-change max change #iterations 4.367142 185.6736 at 10iterations 2.118933 67.57472 at 20iterations 1.042073 33.54873 at 30iterations 0.5097969 15.14713 at 40iterations 0.2496467 8.260880 at 50iterations 0.1215902 3.835211 at 60iterations 5.9606735E-02 1.795563 at 70iterations 2.9227590E-02 0.8737679 at 80iterations 1.4327714E-02 0.4569168 at 90iterations 6.9829370E-03 0.2276192 at 100iterations 3.4330515E-03 0.1111469 at 110iterations 1.6795102E-03 4.9819946E-02 at 120iterations finished qdiffx linear iterations at : 08:21:20 total time elapsed so far: 9.310000 # loops : 120 mean,max change (kT/e) : 1.6795102E-03 4.9819946E-02 energy calculations done at 9.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.480000 DelPhi exited at 08:21:21 9.488u 0.292s 0:10.49 93.1% 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 Tue Oct 11 2011 at 08:21:21 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2104 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.094875 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): -16.31300 29.00000 ymin,ymax (A): -11.48700 36.45300 zmin,zma (A): 0.2650000 52.02800 x,y,z range (A): 45.31300 47.94000 51.76300 scale (grids/A): 3.094875 object centre (A): 6.343500 12.48300 26.14650 number of atom coordinates read : 2104 total number of charged atoms : 2005 net assigned charge : 2.000009 assigned positive charge : 316.1715 centred at (gu) : 91.97862 89.94881 87.70382 assigned negative charge : -314.1719 centred at (gu) : 92.12129 90.07860 86.48820 start vw surface at 0.1600000 fill in re-entrant regions at 0.9500000 boundary points on vw surface= 171131 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19773 grid for indexing accessible points = 1.400000 m= 86409 mr = 123293 m= 33557 mr = 70325 m= 8710 mr = 26751 m= 1338 mr = 6462 m= 97 mr = 761 m= 11 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 1546 time to turn everything in is 2.110000 number of dielectric boundary points 73623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 16040 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) : 2.063250 object centre at (A) : 6.343500 12.48300 26.14650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7686944 0.7645019 midg,1,midg; midg,igrid,midg 0.1366407 -0.2934548 1,midg,midg; igrid,midg,midg 0.1040229 -0.1258137 gauss-seidel spectral radius is 0.9993021 estimated iterations to convergence 299 setup time was (sec) 2.430000 now iterating at: 08:21:23 rms-change max change #iterations 10.04965 456.0105 at 10iterations 5.938250 134.3174 at 20iterations 3.506558 73.45570 at 30iterations 2.071601 41.74476 at 40iterations 1.221995 25.53289 at 50iterations 0.7154424 13.49519 at 60iterations 0.4202152 7.235153 at 70iterations 0.2455192 5.222756 at 80iterations 0.1441089 2.663882 at 90iterations 8.4286749E-02 1.432630 at 100iterations 4.9377546E-02 0.9209900 at 110iterations 2.8750889E-02 0.5016518 at 120iterations 1.6819442E-02 0.3002136 at 130iterations 9.8386435E-03 0.1734028 at 140iterations 5.7370733E-03 9.6332550E-02 at 150iterations 3.3572852E-03 5.9585571E-02 at 160iterations 1.9600671E-03 3.6643982E-02 at 170iterations 1.1464539E-03 2.3034573E-02 at 180iterations finished qdiffx linear iterations at : 08:21:37 total time elapsed so far: 16.21000 # loops : 180 mean,max change (kT/e) : 1.1464539E-03 2.3034573E-02 energy calculations done at 16.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.38000 DelPhi exited at 08:21:38 16.380u 0.319s 0:17.14 97.3% 0+0k 0+0io 0pf+0w