Tue Oct 11 06:11:02 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 06:11:02 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2259 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7068541 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): 20.17000 64.03600 ymin,ymax (A): -3.539000 33.47700 zmin,zma (A): 19.62400 69.98800 x,y,z range (A): 43.86600 37.01600 50.36400 scale (grids/A): 0.7068541 object centre (A): 42.10300 14.96900 44.80600 number of atom coordinates read : 2259 total number of charged atoms : 1941 net assigned charge : 6.500009 assigned positive charge : 313.6040 centred at (gu) : 89.77718 89.68214 89.53842 assigned negative charge : -307.1042 centred at (gu) : 89.90080 89.71024 89.47964 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6987 nv = 96 ne = 84 npr = 41727 no. pairs analyzed = 41727 no. exposed pairs = 2530 no. arc points = 17053 no. surface atoms = 852 nbur = 1407 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 4019 m= 5 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1529 ## 129 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7762 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7834552E-08 7.5213279E-08 midg,1,midg; midg,igrid,midg 7.1768092E-08 3.8250569E-08 1,midg,midg; igrid,midg,midg 1.1775069E-07 -5.6531393E-09 gauss-seidel spectral radius is 0.9895653 estimated iterations to convergence 80 setup time was (sec) 0.5100000 now iterating at: 06:11:03 rms-change max change #iterations 0.2000562 28.08744 at 10iterations 2.4931623E-02 3.735311 at 20iterations 3.2690153E-03 0.4977951 at 30iterations 5.2224693E-04 7.2944641E-02 at 40iterations 1.1956449E-04 1.6538620E-02 at 50iterations finished qdiffx linear iterations at : 06:11:05 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 1.1956449E-04 1.6538620E-02 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 06:11:05 3.113u 0.142s 0:03.60 90.2% 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 Tue Oct 11 2011 at 06:11:06 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2259 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.120562 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): 20.17000 64.03600 ymin,ymax (A): -3.539000 33.47700 zmin,zma (A): 19.62400 69.98800 x,y,z range (A): 43.86600 37.01600 50.36400 scale (grids/A): 2.120562 object centre (A): 42.10300 14.96900 44.80600 number of atom coordinates read : 2259 total number of charged atoms : 1941 net assigned charge : 6.500009 assigned positive charge : 313.6040 centred at (gu) : 89.33133 89.04642 88.61545 assigned negative charge : -307.1042 centred at (gu) : 89.70255 89.13087 88.43908 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17053 grid for indexing accessible points = 1.400000 m= 29951 mr = 53176 m= 5740 mr = 22873 m= 574 mr = 3752 m= 17 mr = 317 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 30769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 15282 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) : 0.7068541 object centre at (A) : 42.10300 14.96900 44.80600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5055567E-02 6.5465033E-02 midg,1,midg; midg,igrid,midg 2.6259929E-02 1.2731139E-02 1,midg,midg; igrid,midg,midg 3.6496054E-02 1.5222729E-02 gauss-seidel spectral radius is 0.9988267 estimated iterations to convergence 231 setup time was (sec) 0.8200000 now iterating at: 06:11:07 rms-change max change #iterations 4.544985 186.4038 at 10iterations 2.253164 68.97791 at 20iterations 1.113494 32.57891 at 30iterations 0.5528099 16.92439 at 40iterations 0.2738129 8.594878 at 50iterations 0.1361214 4.169240 at 60iterations 6.7405425E-02 2.180817 at 70iterations 3.3541210E-02 1.107548 at 80iterations 1.6711516E-02 0.5284805 at 90iterations 8.3243232E-03 0.2503372 at 100iterations 4.1695382E-03 0.1373873 at 110iterations 2.1131253E-03 6.0607910E-02 at 120iterations finished qdiffx linear iterations at : 06:11:13 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 2.1131253E-03 6.0607910E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 06:11:14 7.552u 0.225s 0:08.35 93.0% 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 06:11:14 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2259 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.180844 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): 20.17000 64.03600 ymin,ymax (A): -3.539000 33.47700 zmin,zma (A): 19.62400 69.98800 x,y,z range (A): 43.86600 37.01600 50.36400 scale (grids/A): 3.180844 object centre (A): 42.10300 14.96900 44.80600 number of atom coordinates read : 2259 total number of charged atoms : 1941 net assigned charge : 6.500009 assigned positive charge : 313.6040 centred at (gu) : 88.99715 88.56961 87.92320 assigned negative charge : -307.1042 centred at (gu) : 89.55389 88.69648 87.65870 start vw surface at 0.1600000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 172246 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17053 grid for indexing accessible points = 1.400000 m= 93537 mr = 128296 m= 37713 mr = 78068 m= 10799 mr = 31102 m= 2180 mr = 8250 m= 300 mr = 1569 m= 7 mr = 206 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.740000 number of dielectric boundary points 69291 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 15526 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) : 2.120562 object centre at (A) : 42.10300 14.96900 44.80600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2613376 0.5668795 midg,1,midg; midg,igrid,midg 0.2114952 0.1011154 1,midg,midg; igrid,midg,midg 0.2916619 0.2794313 gauss-seidel spectral radius is 0.9992933 estimated iterations to convergence 297 setup time was (sec) 2.050000 now iterating at: 06:11:16 rms-change max change #iterations 10.17957 361.2542 at 10iterations 6.026387 122.6840 at 20iterations 3.558993 68.94527 at 30iterations 2.097576 42.51772 at 40iterations 1.234025 27.01057 at 50iterations 0.7253511 13.34561 at 60iterations 0.4258923 8.277777 at 70iterations 0.2500152 5.365746 at 80iterations 0.1464376 2.588860 at 90iterations 8.5629746E-02 1.476742 at 100iterations 5.0382890E-02 0.8667107 at 110iterations 2.9634742E-02 0.5128286 at 120iterations 1.7574525E-02 0.3425713 at 130iterations 1.0535433E-02 0.1959038 at 140iterations 6.4721149E-03 0.1273651 at 150iterations 4.0892572E-03 7.6652527E-02 at 160iterations 2.7270508E-03 5.1391602E-02 at 170iterations 1.9232648E-03 3.7742615E-02 at 180iterations finished qdiffx linear iterations at : 06:11:30 total time elapsed so far: 15.88000 # loops : 180 mean,max change (kT/e) : 1.9232648E-03 3.7742615E-02 energy calculations done at 15.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.06000 DelPhi exited at 06:11:31 16.058u 0.260s 0:16.69 97.7% 0+0k 0+0io 0pf+0w