Tue Oct 11 05:27:43 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 Tue Oct 11 2011 at 05:27:43 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 = 2049 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: 0.7343840 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): -6.243000 40.36000 ymin,ymax (A): 11.95000 60.42600 zmin,zma (A): 3.909000 46.47000 x,y,z range (A): 46.60300 48.47600 42.56100 scale (grids/A): 0.7343840 object centre (A): 17.05850 36.18800 25.18950 number of atom coordinates read : 2049 total number of charged atoms : 1921 net assigned charge : 7.500009 assigned positive charge : 310.2271 centred at (gu) : 89.16788 91.04307 90.09325 assigned negative charge : -302.7272 centred at (gu) : 89.28651 90.91441 90.17532 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7641 nv = 96 ne = 84 npr = 41306 no. pairs analyzed = 41306 no. exposed pairs = 2534 no. arc points = 17187 no. surface atoms = 867 nbur = 1182 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 548 mr = 4435 m= 5 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3641 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1494 ## 124 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8084 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8127420E-07 4.4702425E-08 midg,1,midg; midg,igrid,midg 3.9468246E-09 2.7197567E-07 1,midg,midg; igrid,midg,midg 2.5148572E-07 1.1344343E-08 gauss-seidel spectral radius is 0.9903257 estimated iterations to convergence 83 setup time was (sec) 0.5700000 now iterating at: 05:27:44 rms-change max change #iterations 0.2342172 32.75148 at 10iterations 3.1390425E-02 4.928612 at 20iterations 4.3465528E-03 0.5430374 at 30iterations 7.3404156E-04 8.8026047E-02 at 40iterations 1.8355568E-04 2.1141052E-02 at 50iterations finished qdiffx linear iterations at : 05:27:48 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 1.8355568E-04 2.1141052E-02 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 05:27:49 4.465u 0.391s 0:05.23 92.7% 0+0k 0+0io 6pf+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 05:27:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2049 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: 2.203152 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): -6.243000 40.36000 ymin,ymax (A): 11.95000 60.42600 zmin,zma (A): 3.909000 46.47000 x,y,z range (A): 46.60300 48.47600 42.56100 scale (grids/A): 2.203152 object centre (A): 17.05850 36.18800 25.18950 number of atom coordinates read : 2049 total number of charged atoms : 1921 net assigned charge : 7.500009 assigned positive charge : 310.2271 centred at (gu) : 87.50417 93.12952 90.27998 assigned negative charge : -302.7272 centred at (gu) : 87.85969 92.74320 90.52598 start vw surface at 0.1000000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79912 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17187 grid for indexing accessible points = 1.400000 m= 34043 mr = 57026 m= 7121 mr = 26205 m= 715 mr = 4897 m= 26 mr = 354 m= 0 mr = 6 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 33329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15284 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) : 0.7343840 object centre at (A) : 17.05850 36.18800 25.18950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4364183E-02 2.6501868E-02 midg,1,midg; midg,igrid,midg 4.2156830E-02 0.1173696 1,midg,midg; igrid,midg,midg 4.4824965E-02 -4.9957998E-02 gauss-seidel spectral radius is 0.9989004 estimated iterations to convergence 239 setup time was (sec) 0.9800000 now iterating at: 05:27:50 rms-change max change #iterations 4.835005 212.8517 at 10iterations 2.439953 82.68656 at 20iterations 1.239674 43.02679 at 30iterations 0.6282742 19.30390 at 40iterations 0.3191859 8.982188 at 50iterations 0.1621276 4.769421 at 60iterations 8.2076736E-02 2.381920 at 70iterations 4.1839588E-02 1.149454 at 80iterations 2.1331549E-02 0.5862160 at 90iterations 1.0866042E-02 0.2989693 at 100iterations 5.5950549E-03 0.1604252 at 110iterations 2.9316670E-03 8.6335182E-02 at 120iterations finished qdiffx linear iterations at : 05:28:00 total time elapsed so far: 10.49000 # loops : 120 mean,max change (kT/e) : 2.9316670E-03 8.6335182E-02 energy calculations done at 10.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.64000 DelPhi exited at 05:28:00 10.648u 0.466s 0:11.48 96.6% 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 Tue Oct 11 2011 at 05:28:00 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 = 2049 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: 3.304728 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): -6.243000 40.36000 ymin,ymax (A): 11.95000 60.42600 zmin,zma (A): 3.909000 46.47000 x,y,z range (A): 46.60300 48.47600 42.56100 scale (grids/A): 3.304728 object centre (A): 17.05850 36.18800 25.18950 number of atom coordinates read : 2049 total number of charged atoms : 1921 net assigned charge : 7.500009 assigned positive charge : 310.2271 centred at (gu) : 86.25616 94.69417 90.41993 assigned negative charge : -302.7272 centred at (gu) : 86.78959 94.11491 90.78902 start vw surface at 0.1000000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 183656 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17187 grid for indexing accessible points = 1.400000 m= 103681 mr = 136665 m= 45141 mr = 86788 m= 13727 mr = 37580 m= 2908 mr = 10835 m= 354 mr = 2134 m= 23 mr = 215 m= 0 mr = 9 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.150000 number of dielectric boundary points 75264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.340000 number of grid points assigned charge 15367 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) : 2.203152 object centre at (A) : 17.05850 36.18800 25.18950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1556109 0.2255353 midg,1,midg; midg,igrid,midg 0.3195472 0.8811657 1,midg,midg; igrid,midg,midg 0.3799343 -0.5805259 gauss-seidel spectral radius is 0.9993151 estimated iterations to convergence 301 setup time was (sec) 2.540000 now iterating at: 05:28:03 rms-change max change #iterations 10.57191 313.3624 at 10iterations 6.309776 157.8851 at 20iterations 3.762859 69.04463 at 30iterations 2.236266 41.98624 at 40iterations 1.328535 27.61509 at 50iterations 0.7852731 14.88758 at 60iterations 0.4653199 7.594581 at 70iterations 0.2751801 4.929050 at 80iterations 0.1623737 2.921713 at 90iterations 9.6251421E-02 1.549770 at 100iterations 5.6805290E-02 0.9488578 at 110iterations 3.3811565E-02 0.6236038 at 120iterations 2.0164795E-02 0.3318588 at 130iterations 1.2215677E-02 0.2191467 at 140iterations 7.5723799E-03 0.1336670 at 150iterations 4.8889131E-03 8.5441589E-02 at 160iterations 3.3338098E-03 5.9448242E-02 at 170iterations 2.4283791E-03 3.9493561E-02 at 180iterations finished qdiffx linear iterations at : 05:28:19 total time elapsed so far: 18.50000 # loops : 180 mean,max change (kT/e) : 2.4283791E-03 3.9493561E-02 energy calculations done at 18.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.68000 DelPhi exited at 05:28:20 18.682u 0.485s 0:19.46 98.4% 0+0k 0+0io 0pf+0w