Mon Oct 10 13:58:44 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 Mon Oct 10 2011 at 13:58:44 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 = 2612 !!! WARNING: SER 2 has a net charge of 0.5000 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: 0.6170164 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): -31.35700 17.54200 ymin,ymax (A): -23.56900 22.60500 zmin,zma (A): -12.47800 45.21900 x,y,z range (A): 48.89900 46.17400 57.69700 scale (grids/A): 0.6170164 object centre (A): -6.907500 -0.4820004 16.37050 number of atom coordinates read : 2612 total number of charged atoms : 2472 net assigned charge : 4.500011 assigned positive charge : 393.5650 centred at (gu) : 88.56808 89.33435 89.54876 assigned negative charge : -389.0655 centred at (gu) : 88.43311 89.37979 89.43725 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6381 nv = 96 ne = 84 npr = 55147 no. pairs analyzed = 55147 no. exposed pairs = 2978 no. arc points = 21408 no. surface atoms = 1006 nbur = 1606 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 291 mr = 3510 m= 0 mr = 33 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 131 time to turn everything in is 0.3100000 number of dielectric boundary points 3129 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2214 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8046 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8102708E-09 9.1949142E-09 midg,1,midg; midg,igrid,midg 7.1860695E-09 6.0148431E-10 1,midg,midg; igrid,midg,midg -6.8568906E-09 8.4264311E-09 gauss-seidel spectral radius is 0.9863935 estimated iterations to convergence 70 setup time was (sec) 0.6100000 now iterating at: 13:58:45 rms-change max change #iterations 0.1241383 20.60032 at 10iterations 1.1250759E-02 1.551437 at 20iterations 1.0430230E-03 0.1630135 at 30iterations 9.5314674E-05 1.5657425E-02 at 40iterations 8.7418948E-06 1.3389587E-03 at 50iterations finished qdiffx linear iterations at : 13:58:49 total time elapsed so far: 4.690000 # loops : 50 mean,max change (kT/e) : 8.7418948E-06 1.3389587E-03 energy calculations done at 4.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.860000 DelPhi exited at 13:58:50 4.869u 0.374s 0:05.88 88.9% 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 Mon Oct 10 2011 at 13:58:50 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 = 2612 !!! WARNING: SER 2 has a net charge of 0.5000 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: 1.851049 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): -31.35700 17.54200 ymin,ymax (A): -23.56900 22.60500 zmin,zma (A): -12.47800 45.21900 x,y,z range (A): 48.89900 46.17400 57.69700 scale (grids/A): 1.851049 object centre (A): -6.907500 -0.4820004 16.37050 number of atom coordinates read : 2612 total number of charged atoms : 2472 net assigned charge : 4.500011 assigned positive charge : 393.5650 centred at (gu) : 85.70367 88.00263 88.64564 assigned negative charge : -389.0655 centred at (gu) : 85.29906 88.13918 88.31149 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21408 grid for indexing accessible points = 1.400000 m= 23400 mr = 48923 m= 3144 mr = 17223 m= 143 mr = 1897 m= 0 mr = 41 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 4905 time to turn everything in is 0.5600000 number of dielectric boundary points 28571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19385 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) : 0.6170164 object centre at (A) : -6.907500 -0.4820004 16.37050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2797225E-02 2.5957623E-02 midg,1,midg; midg,igrid,midg 1.0946754E-02 2.4436431E-03 1,midg,midg; igrid,midg,midg -2.9079218E-03 4.0261261E-02 gauss-seidel spectral radius is 0.9985527 estimated iterations to convergence 208 setup time was (sec) 0.8600000 now iterating at: 13:58:51 rms-change max change #iterations 3.976517 160.0475 at 10iterations 1.823395 66.24547 at 20iterations 0.8340246 28.40690 at 30iterations 0.3822367 13.91918 at 40iterations 0.1756248 6.004837 at 50iterations 8.0215134E-02 2.640034 at 60iterations 3.6856182E-02 1.226213 at 70iterations 1.6841438E-02 0.5456543 at 80iterations 7.7394913E-03 0.2383487 at 90iterations 3.5350055E-03 0.1173718 at 100iterations 1.6151350E-03 5.1265717E-02 at 110iterations 7.4439775E-04 2.6153564E-02 at 120iterations finished qdiffx linear iterations at : 13:59:02 total time elapsed so far: 11.68000 # loops : 120 mean,max change (kT/e) : 7.4439775E-04 2.6153564E-02 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.85000 DelPhi exited at 13:59:03 11.852u 0.436s 0:13.13 93.5% 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 Mon Oct 10 2011 at 13:59:03 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 = 2612 !!! WARNING: SER 2 has a net charge of 0.5000 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: 2.776574 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): -31.35700 17.54200 ymin,ymax (A): -23.56900 22.60500 zmin,zma (A): -12.47800 45.21900 x,y,z range (A): 48.89900 46.17400 57.69700 scale (grids/A): 2.776574 object centre (A): -6.907500 -0.4820004 16.37050 number of atom coordinates read : 2612 total number of charged atoms : 2472 net assigned charge : 4.500011 assigned positive charge : 393.5650 centred at (gu) : 83.55528 87.00376 87.96832 assigned negative charge : -389.0655 centred at (gu) : 82.94854 87.20870 87.46720 start vw surface at 0.1200000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 162330 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21408 grid for indexing accessible points = 1.400000 m= 78601 mr = 118611 m= 25538 mr = 64584 m= 5415 mr = 20464 m= 652 mr = 4076 m= 21 mr = 434 m= 0 mr = 5 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 17295 time to turn everything in is 1.440000 number of dielectric boundary points 64383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 19773 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) : 1.851049 object centre at (A) : -6.907500 -0.4820004 16.37050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5672797E-02 0.3381998 midg,1,midg; midg,igrid,midg 0.1328987 1.5677972E-02 1,midg,midg; igrid,midg,midg -2.0895597E-02 0.5459194 gauss-seidel spectral radius is 0.9992292 estimated iterations to convergence 284 setup time was (sec) 1.770000 now iterating at: 13:59:05 rms-change max change #iterations 9.378826 372.9463 at 10iterations 5.385348 134.0433 at 20iterations 3.068907 77.25237 at 30iterations 1.748320 37.25862 at 40iterations 0.9941725 19.68002 at 50iterations 0.5661613 10.30440 at 60iterations 0.3216174 7.928493 at 70iterations 0.1824182 3.522489 at 80iterations 0.1037042 1.887272 at 90iterations 5.8979210E-02 1.145041 at 100iterations 3.3444107E-02 0.6441422 at 110iterations 1.8948285E-02 0.3821030 at 120iterations 1.0770277E-02 0.2147846 at 130iterations 6.1249961E-03 0.1096783 at 140iterations 3.4666760E-03 7.8496933E-02 at 150iterations 1.9701724E-03 3.5860538E-02 at 160iterations 1.1168189E-03 1.9741058E-02 at 170iterations 6.3495629E-04 1.1734009E-02 at 180iterations finished qdiffx linear iterations at : 13:59:23 total time elapsed so far: 19.89000 # loops : 180 mean,max change (kT/e) : 6.3495629E-04 1.1734009E-02 energy calculations done at 19.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.06000 DelPhi exited at 13:59:24 20.063u 0.471s 0:21.21 96.7% 0+0k 0+0io 0pf+0w