Tue Oct 11 03:35:32 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 03:35:32 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 !!! WARNING: HIQ 435 has a net charge of 0.5140 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: 0.6146514 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): 21.67400 69.53500 ymin,ymax (A): -15.19400 33.11600 zmin,zma (A): -9.466001 48.45300 x,y,z range (A): 47.86100 48.31000 57.91900 scale (grids/A): 0.6146514 object centre (A): 45.60450 8.961000 19.49350 number of atom coordinates read : 2128 total number of charged atoms : 2029 net assigned charge : -5.985984 assigned positive charge : 316.1206 centred at (gu) : 90.47884 89.93166 90.65137 assigned negative charge : -322.1068 centred at (gu) : 90.50750 89.90820 90.60106 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5486 nv = 96 ne = 84 npr = 43518 no. pairs analyzed = 43518 no. exposed pairs = 2663 no. arc points = 19091 no. surface atoms = 895 nbur = 1233 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 294 mr = 2961 m= 0 mr = 32 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.1600000 number of dielectric boundary points 2787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1820 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6230998E-09 -1.9749731E-09 midg,1,midg; midg,igrid,midg -5.2816187E-09 -2.9483693E-09 1,midg,midg; igrid,midg,midg -2.4859415E-09 -6.0512799E-09 gauss-seidel spectral radius is 0.9862593 estimated iterations to convergence 70 setup time was (sec) 0.3400000 now iterating at: 03:35:33 rms-change max change #iterations 0.1134733 19.27271 at 10iterations 1.0111935E-02 1.689609 at 20iterations 8.8878896E-04 0.1393356 at 30iterations 7.9279205E-05 1.4647484E-02 at 40iterations 7.2685393E-06 1.2893677E-03 at 50iterations finished qdiffx linear iterations at : 03:35:35 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 7.2685393E-06 1.2893677E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 03:35:36 3.291u 0.177s 0:03.95 87.5% 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 Oct 11 2011 at 03:35:36 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 !!! WARNING: HIQ 435 has a net charge of 0.5140 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: 1.843954 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): 21.67400 69.53500 ymin,ymax (A): -15.19400 33.11600 zmin,zma (A): -9.466001 48.45300 x,y,z range (A): 47.86100 48.31000 57.91900 scale (grids/A): 1.843954 object centre (A): 45.60450 8.961000 19.49350 number of atom coordinates read : 2128 total number of charged atoms : 2029 net assigned charge : -5.985984 assigned positive charge : 316.1206 centred at (gu) : 91.43620 89.79464 91.95375 assigned negative charge : -322.1068 centred at (gu) : 91.52238 89.72443 91.80305 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 59146 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19091 grid for indexing accessible points = 1.400000 m= 20324 mr = 40229 m= 2871 mr = 14854 m= 121 mr = 1742 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 1633 time to turn everything in is 0.2900000 number of dielectric boundary points 25609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 15902 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) : 0.6146514 object centre at (A) : 45.60450 8.961000 19.49350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1667866E-02 1.1400708E-03 midg,1,midg; midg,igrid,midg -6.4918310E-03 -1.4966520E-02 1,midg,midg; igrid,midg,midg -1.5550426E-03 2.1484483E-03 gauss-seidel spectral radius is 0.9984989 estimated iterations to convergence 205 setup time was (sec) 0.4900000 now iterating at: 03:35:37 rms-change max change #iterations 3.584731 177.1199 at 10iterations 1.619969 63.51559 at 20iterations 0.7289962 28.09228 at 30iterations 0.3286117 11.29644 at 40iterations 0.1480360 5.668704 at 50iterations 6.6476151E-02 2.690590 at 60iterations 3.0003786E-02 1.027814 at 70iterations 1.3525850E-02 0.5078077 at 80iterations 6.1183451E-03 0.2359991 at 90iterations 2.7595581E-03 9.2555046E-02 at 100iterations 1.2432378E-03 4.2871475E-02 at 110iterations 5.6107994E-04 2.1203995E-02 at 120iterations finished qdiffx linear iterations at : 03:35:44 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 5.6107994E-04 2.1203995E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 03:35:44 7.521u 0.200s 0:08.10 95.3% 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 Tue Oct 11 2011 at 03:35:44 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 !!! WARNING: HIQ 435 has a net charge of 0.5140 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: 2.765932 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): 21.67400 69.53500 ymin,ymax (A): -15.19400 33.11600 zmin,zma (A): -9.466001 48.45300 x,y,z range (A): 47.86100 48.31000 57.91900 scale (grids/A): 2.765932 object centre (A): 45.60450 8.961000 19.49350 number of atom coordinates read : 2128 total number of charged atoms : 2029 net assigned charge : -5.985984 assigned positive charge : 316.1206 centred at (gu) : 92.15428 89.69200 92.93069 assigned negative charge : -322.1068 centred at (gu) : 92.28352 89.58662 92.70453 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 137175 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19091 grid for indexing accessible points = 1.400000 m= 66205 mr = 98070 m= 23370 mr = 53693 m= 4958 mr = 18767 m= 583 mr = 3592 m= 29 mr = 376 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 5604 time to turn everything in is 0.7400000 number of dielectric boundary points 57814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 16231 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) : 1.843954 object centre at (A) : 45.60450 8.961000 19.49350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4044398 5.9675734E-02 midg,1,midg; midg,igrid,midg 7.1027249E-02 -0.1722013 1,midg,midg; igrid,midg,midg 2.6527870E-02 0.1174426 gauss-seidel spectral radius is 0.9992126 estimated iterations to convergence 281 setup time was (sec) 0.9700000 now iterating at: 03:35:45 rms-change max change #iterations 8.462756 278.6376 at 10iterations 4.800803 107.7044 at 20iterations 2.713042 55.79935 at 30iterations 1.529048 32.15617 at 40iterations 0.8610395 17.10992 at 50iterations 0.4845318 11.51858 at 60iterations 0.2733983 6.128654 at 70iterations 0.1537060 4.016563 at 80iterations 8.6653978E-02 1.850340 at 90iterations 4.8669826E-02 0.9985847 at 100iterations 2.7421270E-02 0.5845308 at 110iterations 1.5431525E-02 0.3321609 at 120iterations 8.6980248E-03 0.1658845 at 130iterations 4.8928643E-03 9.8255157E-02 at 140iterations 2.7554107E-03 5.0557971E-02 at 150iterations 1.5547818E-03 3.4463882E-02 at 160iterations 8.7419414E-04 1.9760132E-02 at 170iterations 4.9271708E-04 1.0753632E-02 at 180iterations finished qdiffx linear iterations at : 03:35:56 total time elapsed so far: 11.83000 # loops : 180 mean,max change (kT/e) : 4.9271708E-04 1.0753632E-02 energy calculations done at 11.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.95000 DelPhi exited at 03:35:57 11.955u 0.196s 0:12.46 97.4% 0+0k 0+0io 0pf+0w