Sun Oct 9 10:15:37 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 Sun Oct 9 2011 at 10:15:37 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 !!! WARNING: HIR 524 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: 0.6448925 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): -17.85100 31.18100 ymin,ymax (A): 19.17900 74.38200 zmin,zma (A): -2.570000 48.26800 x,y,z range (A): 49.03200 55.20300 50.83800 scale (grids/A): 0.6448925 object centre (A): 6.665000 46.78050 22.84900 number of atom coordinates read : 2057 total number of charged atoms : 1920 net assigned charge : -2.757985 assigned positive charge : 298.6057 centred at (gu) : 89.20418 89.51242 90.71606 assigned negative charge : -301.3643 centred at (gu) : 89.16656 89.78576 90.53687 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5826 nv = 96 ne = 84 npr = 41803 no. pairs analyzed = 41803 no. exposed pairs = 2763 no. arc points = 18941 no. surface atoms = 929 nbur = 1128 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3060 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.1700000 number of dielectric boundary points 3033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1753 ## 128 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6782 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0336451E-08 1.5639447E-08 midg,1,midg; midg,igrid,midg 2.5161293E-08 -3.0544449E-08 1,midg,midg; igrid,midg,midg -1.0321747E-08 -8.3345680E-10 gauss-seidel spectral radius is 0.9874987 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 10:15:37 rms-change max change #iterations 0.1341194 25.98947 at 10iterations 1.3436103E-02 2.082030 at 20iterations 1.3552996E-03 0.2125912 at 30iterations 1.3705566E-04 2.2001266E-02 at 40iterations 1.3537634E-05 1.9874573E-03 at 50iterations finished qdiffx linear iterations at : 10:15:40 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.3537634E-05 1.9874573E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 10:15:41 3.450u 0.175s 0:03.91 92.5% 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 Sun Oct 9 2011 at 10:15:41 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 !!! WARNING: HIR 524 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: 1.934677 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): -17.85100 31.18100 ymin,ymax (A): 19.17900 74.38200 zmin,zma (A): -2.570000 48.26800 x,y,z range (A): 49.03200 55.20300 50.83800 scale (grids/A): 1.934677 object centre (A): 6.665000 46.78050 22.84900 number of atom coordinates read : 2057 total number of charged atoms : 1920 net assigned charge : -2.757985 assigned positive charge : 298.6057 centred at (gu) : 87.61232 88.53716 92.14798 assigned negative charge : -301.3643 centred at (gu) : 87.49993 89.35755 91.61073 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 63096 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18941 grid for indexing accessible points = 1.400000 m= 22440 mr = 42773 m= 3617 mr = 16267 m= 244 mr = 2284 m= 3 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 27964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 15109 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) : 0.6448925 object centre at (A) : 6.665000 46.78050 22.84900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2386090E-02 3.0615240E-02 midg,1,midg; midg,igrid,midg 3.2541756E-02 -2.7826196E-02 1,midg,midg; igrid,midg,midg -2.2939909E-02 -1.6598953E-02 gauss-seidel spectral radius is 0.9986252 estimated iterations to convergence 214 setup time was (sec) 0.5400000 now iterating at: 10:15:42 rms-change max change #iterations 3.835184 194.9864 at 10iterations 1.785694 66.97350 at 20iterations 0.8351021 34.00902 at 30iterations 0.3907879 13.64966 at 40iterations 0.1828007 5.948447 at 50iterations 8.5312471E-02 2.837364 at 60iterations 3.9851692E-02 1.266888 at 70iterations 1.8696057E-02 0.6505890 at 80iterations 8.7571554E-03 0.2950668 at 90iterations 4.0712594E-03 0.1401434 at 100iterations 1.9043061E-03 7.1033001E-02 at 110iterations 8.9348381E-04 3.1477213E-02 at 120iterations finished qdiffx linear iterations at : 10:15:49 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 8.9348381E-04 3.1477213E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 10:15:49 8.070u 0.218s 0:08.60 96.2% 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 Sun Oct 9 2011 at 10:15:49 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 !!! WARNING: HIR 524 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: 2.902016 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): -17.85100 31.18100 ymin,ymax (A): 19.17900 74.38200 zmin,zma (A): -2.570000 48.26800 x,y,z range (A): 49.03200 55.20300 50.83800 scale (grids/A): 2.902016 object centre (A): 6.665000 46.78050 22.84900 number of atom coordinates read : 2057 total number of charged atoms : 1920 net assigned charge : -2.757985 assigned positive charge : 298.6057 centred at (gu) : 86.41855 87.80553 93.22202 assigned negative charge : -301.3643 centred at (gu) : 86.24995 89.03628 92.41626 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 145788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18941 grid for indexing accessible points = 1.400000 m= 71891 mr = 103928 m= 26044 mr = 57909 m= 6563 mr = 20743 m= 1074 mr = 5006 m= 85 mr = 776 m= 0 mr = 47 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8300000 number of dielectric boundary points 63036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 15359 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) : 1.934677 object centre at (A) : 6.665000 46.78050 22.84900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5033528 0.3796299 midg,1,midg; midg,igrid,midg 0.3037403 -0.2327555 1,midg,midg; igrid,midg,midg -0.2707796 -0.2096165 gauss-seidel spectral radius is 0.9992506 estimated iterations to convergence 288 setup time was (sec) 1.070000 now iterating at: 10:15:51 rms-change max change #iterations 8.901009 328.2562 at 10iterations 5.160967 116.2967 at 20iterations 2.979731 71.78079 at 30iterations 1.712809 33.38831 at 40iterations 0.9879237 20.03268 at 50iterations 0.5680702 11.79836 at 60iterations 0.3257519 6.427137 at 70iterations 0.1870110 4.054947 at 80iterations 0.1075231 2.404669 at 90iterations 6.1644249E-02 1.232619 at 100iterations 3.5272945E-02 0.7106609 at 110iterations 2.0243416E-02 0.3935013 at 120iterations 1.1600809E-02 0.2346127 at 130iterations 6.6376622E-03 0.1490173 at 140iterations 3.8095233E-03 7.4671745E-02 at 150iterations 2.1753309E-03 3.9970398E-02 at 160iterations 1.2457783E-03 2.4976730E-02 at 170iterations 7.1402220E-04 1.4059067E-02 at 180iterations finished qdiffx linear iterations at : 10:16:03 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 7.1402220E-04 1.4059067E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 10:16:03 13.088u 0.242s 0:13.63 97.7% 0+0k 0+0io 0pf+0w