Sun Oct 9 02:19:13 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+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 Sun Oct 9 2011 at 02:19:13 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2018 !!! WARNING: MG2 215 has a net charge of 1.4000 !!! WARNING: SAM 216 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.3950 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: 0.7158081 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): -32.89800 16.83600 ymin,ymax (A): -29.95400 17.52400 zmin,zma (A): -36.07500 9.286000 x,y,z range (A): 49.73400 47.47800 45.36100 scale (grids/A): 0.7158081 object centre (A): -8.030999 -6.215000 -13.39450 number of atom coordinates read : 2018 total number of charged atoms : 1930 net assigned charge : -5.304992 assigned positive charge : 307.4018 centred at (gu) : 89.15717 89.85758 92.26260 assigned negative charge : -312.7070 centred at (gu) : 89.15955 89.87065 92.21905 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7300 nv = 96 ne = 84 npr = 40959 no. pairs analyzed = 40959 no. exposed pairs = 2285 no. arc points = 16109 no. surface atoms = 773 nbur = 1245 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 505 mr = 4485 m= 2 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 215 time to turn everything in is 0.2900000 number of dielectric boundary points 3206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1350 ## 104 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7898 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2851465E-08 -4.3481638E-08 midg,1,midg; midg,igrid,midg -4.8306539E-08 -6.0900703E-08 1,midg,midg; igrid,midg,midg -6.2473902E-08 -4.8073922E-08 gauss-seidel spectral radius is 0.9898213 estimated iterations to convergence 81 setup time was (sec) 0.5700000 now iterating at: 02:19:14 rms-change max change #iterations 0.2165745 30.75448 at 10iterations 2.7409542E-02 4.095009 at 20iterations 3.4715494E-03 0.4367046 at 30iterations 4.3603507E-04 5.0365090E-02 at 40iterations 5.4959903E-05 7.6847076E-03 at 50iterations finished qdiffx linear iterations at : 02:19:18 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 5.4959903E-05 7.6847076E-03 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.010000 DelPhi exited at 02:19:18 4.011u 0.259s 0:04.54 93.8% 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 Sun Oct 9 2011 at 02:19:18 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2018 !!! WARNING: MG2 215 has a net charge of 1.4000 !!! WARNING: SAM 216 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.3950 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: 2.147424 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): -32.89800 16.83600 ymin,ymax (A): -29.95400 17.52400 zmin,zma (A): -36.07500 9.286000 x,y,z range (A): 49.73400 47.47800 45.36100 scale (grids/A): 2.147424 object centre (A): -8.030999 -6.215000 -13.39450 number of atom coordinates read : 2018 total number of charged atoms : 1930 net assigned charge : -5.304992 assigned positive charge : 307.4018 centred at (gu) : 87.47141 89.57256 96.78779 assigned negative charge : -312.7070 centred at (gu) : 87.47866 89.61206 96.65731 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 77395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16109 grid for indexing accessible points = 1.400000 m= 32318 mr = 56499 m= 6919 mr = 25915 m= 665 mr = 5058 m= 17 mr = 389 m= 0 mr = 2 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 5909 time to turn everything in is 0.6900000 number of dielectric boundary points 29451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 15337 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) : 0.7158081 object centre at (A) : -8.030999 -6.215000 -13.39450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5879868E-02 -1.7854122E-02 midg,1,midg; midg,igrid,midg -4.3689106E-02 -2.0441512E-02 1,midg,midg; igrid,midg,midg -1.7430557E-02 -2.5425954E-02 gauss-seidel spectral radius is 0.9988461 estimated iterations to convergence 233 setup time was (sec) 0.9800000 now iterating at: 02:19:19 rms-change max change #iterations 4.715449 204.9122 at 10iterations 2.347884 73.37304 at 20iterations 1.170399 39.28513 at 30iterations 0.5828986 17.25599 at 40iterations 0.2906086 8.869986 at 50iterations 0.1449899 4.237446 at 60iterations 7.2382152E-02 2.349777 at 70iterations 3.5978559E-02 1.086048 at 80iterations 1.7993361E-02 0.5282497 at 90iterations 8.9563448E-03 0.2595940 at 100iterations 4.4696257E-03 0.1187425 at 110iterations 2.2353586E-03 7.1093559E-02 at 120iterations finished qdiffx linear iterations at : 02:19:28 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 2.2353586E-03 7.1093559E-02 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.370000 DelPhi exited at 02:19:28 9.375u 0.295s 0:10.02 96.4% 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 02:19:28 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2018 !!! WARNING: MG2 215 has a net charge of 1.4000 !!! WARNING: SAM 216 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.3950 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: 3.221136 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): -32.89800 16.83600 ymin,ymax (A): -29.95400 17.52400 zmin,zma (A): -36.07500 9.286000 x,y,z range (A): 49.73400 47.47800 45.36100 scale (grids/A): 3.221136 object centre (A): -8.030999 -6.215000 -13.39450 number of atom coordinates read : 2018 total number of charged atoms : 1930 net assigned charge : -5.304992 assigned positive charge : 307.4018 centred at (gu) : 86.20712 89.35883 100.1817 assigned negative charge : -312.7070 centred at (gu) : 86.21809 89.41808 99.98601 start vw surface at 0.1300000 fill in re-entrant regions at 0.9700000 boundary points on vw surface= 178599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16109 grid for indexing accessible points = 1.400000 m= 98769 mr = 135490 m= 43501 mr = 84763 m= 13481 mr = 37490 m= 2862 mr = 11128 m= 361 mr = 2169 m= 7 mr = 265 m= 0 mr = 3 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 19772 time to turn everything in is 2.210000 number of dielectric boundary points 66272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.360000 number of grid points assigned charge 15440 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) : 2.147424 object centre at (A) : -8.030999 -6.215000 -13.39450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1149056 -0.2847613 midg,1,midg; midg,igrid,midg -0.5416494 -0.2182101 1,midg,midg; igrid,midg,midg 6.3778460E-02 -0.2416181 gauss-seidel spectral radius is 0.9992992 estimated iterations to convergence 298 setup time was (sec) 2.550000 now iterating at: 02:19:31 rms-change max change #iterations 10.32813 406.3747 at 10iterations 6.031197 120.9301 at 20iterations 3.525006 63.34086 at 30iterations 2.063975 36.31730 at 40iterations 1.202719 21.57983 at 50iterations 0.7021580 12.13949 at 60iterations 0.4107547 7.202141 at 70iterations 0.2390120 4.153820 at 80iterations 0.1395894 2.428215 at 90iterations 8.1438527E-02 1.406464 at 100iterations 4.7473419E-02 0.8289261 at 110iterations 2.7647559E-02 0.4560051 at 120iterations 1.6149439E-02 0.2650833 at 130iterations 9.4273621E-03 0.1546745 at 140iterations 5.4945764E-03 9.1629982E-02 at 150iterations 3.1992770E-03 5.4433823E-02 at 160iterations 1.8694754E-03 3.2600597E-02 at 170iterations 1.0925581E-03 1.8583298E-02 at 180iterations finished qdiffx linear iterations at : 02:19:46 total time elapsed so far: 17.57000 # loops : 180 mean,max change (kT/e) : 1.0925581E-03 1.8583298E-02 energy calculations done at 17.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.75000 DelPhi exited at 02:19:46 17.747u 0.318s 0:18.36 98.3% 0+0k 0+0io 0pf+0w