Wed Dec 28 11:01:07 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+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 Wed Dec 28 2011 at 11:01:07 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: 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: 0.6021447 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): -24.12500 34.99700 ymin,ymax (A): -19.71600 20.26100 zmin,zma (A): -2.818000 38.66700 x,y,z range (A): 59.12200 39.97700 41.48500 scale (grids/A): 0.6021447 object centre (A): 5.436001 0.2725000 17.92450 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 89.73789 90.57562 90.24033 assigned negative charge : -285.8263 centred at (gu) : 89.74430 90.68356 90.40137 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4813 nv = 96 ne = 84 npr = 40223 no. pairs analyzed = 40223 no. exposed pairs = 2403 no. arc points = 16976 no. surface atoms = 816 nbur = 1148 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 195 mr = 2649 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 105 time to turn everything in is 0.1700000 number of dielectric boundary points 2341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1808 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 5923 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2025531E-09 -3.9714139E-09 midg,1,midg; midg,igrid,midg 3.5254781E-09 -2.4996862E-09 1,midg,midg; igrid,midg,midg 1.2085943E-09 7.2989903E-10 gauss-seidel spectral radius is 0.9856713 estimated iterations to convergence 68 setup time was (sec) 0.4000000 now iterating at: 11:01:07 rms-change max change #iterations 9.6165165E-02 15.70257 at 10iterations 7.9931859E-03 1.425632 at 20iterations 6.8294437E-04 0.1168022 at 30iterations 5.8835318E-05 1.0044098E-02 at 40iterations 5.0213816E-06 8.1157684E-04 at 50iterations finished qdiffx linear iterations at : 11:01:11 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 5.0213816E-06 8.1157684E-04 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.380000 DelPhi exited at 11:01:12 4.386u 0.311s 0:05.23 89.6% 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 Wed Dec 28 2011 at 11:01:12 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.806434 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): -24.12500 34.99700 ymin,ymax (A): -19.71600 20.26100 zmin,zma (A): -2.818000 38.66700 x,y,z range (A): 59.12200 39.97700 41.48500 scale (grids/A): 1.806434 object centre (A): 5.436001 0.2725000 17.92450 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 89.21378 91.72704 90.72106 assigned negative charge : -285.8263 centred at (gu) : 89.23315 92.05095 91.20412 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 52238 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16976 grid for indexing accessible points = 1.400000 m= 18322 mr = 36023 m= 2358 mr = 13931 m= 74 mr = 1489 m= 0 mr = 16 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1032 time to turn everything in is 0.3100000 number of dielectric boundary points 21533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 14322 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) : 0.6021447 object centre at (A) : 5.436001 0.2725000 17.92450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5018966E-03 -1.0129690E-02 midg,1,midg; midg,igrid,midg 5.4606427E-03 -4.7817803E-03 1,midg,midg; igrid,midg,midg 4.2417821E-02 2.8906703E-02 gauss-seidel spectral radius is 0.9984053 estimated iterations to convergence 199 setup time was (sec) 0.6900000 now iterating at: 11:01:13 rms-change max change #iterations 3.211509 168.6183 at 10iterations 1.414230 57.53143 at 20iterations 0.6226591 23.86771 at 30iterations 0.2730160 10.71067 at 40iterations 0.1203585 4.756935 at 50iterations 5.3040605E-02 1.936002 at 60iterations 2.3418518E-02 0.9322128 at 70iterations 1.0283921E-02 0.4084702 at 80iterations 4.5469659E-03 0.1688843 at 90iterations 1.9915425E-03 7.6476574E-02 at 100iterations 8.7998109E-04 3.6088228E-02 at 110iterations 3.8847281E-04 1.6088963E-02 at 120iterations finished qdiffx linear iterations at : 11:01:22 total time elapsed so far: 9.750000 # loops : 120 mean,max change (kT/e) : 3.8847281E-04 1.6088963E-02 energy calculations done at 9.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.870000 DelPhi exited at 11:01:23 9.872u 0.491s 0:11.34 91.3% 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 Wed Dec 28 2011 at 11:01:24 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.709651 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): -24.12500 34.99700 ymin,ymax (A): -19.71600 20.26100 zmin,zma (A): -2.818000 38.66700 x,y,z range (A): 59.12200 39.97700 41.48500 scale (grids/A): 2.709651 object centre (A): 5.436001 0.2725000 17.92450 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 88.82066 92.59040 91.08157 assigned negative charge : -285.8263 centred at (gu) : 88.84988 93.07649 91.80628 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 120738 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16976 grid for indexing accessible points = 1.400000 m= 60419 mr = 87044 m= 20518 mr = 50320 m= 4129 mr = 16931 m= 350 mr = 3189 m= 5 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 3421 time to turn everything in is 0.7500000 number of dielectric boundary points 48494 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.8500000 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) : 1.806434 object centre at (A) : 5.436001 0.2725000 17.92450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2758643E-02 -0.1024647 midg,1,midg; midg,igrid,midg 4.4247847E-02 -4.2630862E-02 1,midg,midg; igrid,midg,midg 0.4689141 0.3031574 gauss-seidel spectral radius is 0.9991737 estimated iterations to convergence 275 setup time was (sec) 1.030000 now iterating at: 11:01:25 rms-change max change #iterations 7.680837 290.3813 at 10iterations 4.301972 117.9694 at 20iterations 2.404942 59.85975 at 30iterations 1.331476 30.74072 at 40iterations 0.7411277 15.99065 at 50iterations 0.4109633 9.268875 at 60iterations 0.2286935 4.939679 at 70iterations 0.1269477 3.224220 at 80iterations 7.0196897E-02 1.591560 at 90iterations 3.9001632E-02 0.9575319 at 100iterations 2.1630833E-02 0.5075836 at 110iterations 1.2026387E-02 0.2604213 at 120iterations 6.6741705E-03 0.1505027 at 130iterations 3.7036738E-03 7.8958511E-02 at 140iterations 2.0537460E-03 4.7851563E-02 at 150iterations 1.1429540E-03 2.6012421E-02 at 160iterations 6.3326076E-04 1.4551878E-02 at 170iterations 3.5214689E-04 7.5259209E-03 at 180iterations finished qdiffx linear iterations at : 11:01:38 total time elapsed so far: 14.19000 # loops : 180 mean,max change (kT/e) : 3.5214689E-04 7.5259209E-03 energy calculations done at 14.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.31000 DelPhi exited at 11:01:39 14.311u 0.434s 0:15.22 96.8% 0+0k 0+0io 0pf+0w