Mon Oct 10 22:45:46 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+sph2.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 = amb2.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 22:45:46 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2746 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6355327 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): -8.335999 47.68000 ymin,ymax (A): -15.45100 31.46800 zmin,zma (A): -11.82000 41.53400 x,y,z range (A): 56.01600 46.91900 53.35400 scale (grids/A): 0.6355327 object centre (A): 19.67200 8.008501 14.85700 number of atom coordinates read : 2746 total number of charged atoms : 2595 net assigned charge : 5.312014 assigned positive charge : 416.1705 centred at (gu) : 89.45277 89.89052 89.08493 assigned negative charge : -410.8593 centred at (gu) : 89.73918 89.89149 89.13379 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7434 nv = 96 ne = 84 npr = 54939 no. pairs analyzed = 54939 no. exposed pairs = 3271 no. arc points = 22574 no. surface atoms = 1109 nbur = 1637 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 4259 m= 0 mr = 41 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 46 time to turn everything in is 0.4100000 number of dielectric boundary points 3498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2191 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8921 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4478249E-08 1.0668377E-09 midg,1,midg; midg,igrid,midg 6.8540280E-09 6.3430949E-09 1,midg,midg; igrid,midg,midg 4.1589107E-08 -2.2747313E-08 gauss-seidel spectral radius is 0.9871845 estimated iterations to convergence 72 setup time was (sec) 0.7100000 now iterating at: 22:45:47 rms-change max change #iterations 0.1507946 23.53811 at 10iterations 1.5672844E-02 2.609787 at 20iterations 1.9776879E-03 0.3232975 at 30iterations 4.3660394E-04 9.3048096E-02 at 40iterations 1.2722843E-04 2.8011322E-02 at 50iterations finished qdiffx linear iterations at : 22:45:51 total time elapsed so far: 4.220000 # loops : 50 mean,max change (kT/e) : 1.2722843E-04 2.8011322E-02 energy calculations done at 4.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 22:45:51 4.423u 0.433s 0:05.26 92.2% 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 Mon Oct 10 2011 at 22:45:51 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2746 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 1.906598 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): -8.335999 47.68000 ymin,ymax (A): -15.45100 31.46800 zmin,zma (A): -11.82000 41.53400 x,y,z range (A): 56.01600 46.91900 53.35400 scale (grids/A): 1.906598 object centre (A): 19.67200 8.008501 14.85700 number of atom coordinates read : 2746 total number of charged atoms : 2595 net assigned charge : 5.312014 assigned positive charge : 416.1705 centred at (gu) : 88.35760 89.67117 87.25425 assigned negative charge : -410.8593 centred at (gu) : 89.21726 89.67432 87.40122 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 80429 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22574 grid for indexing accessible points = 1.400000 m= 29294 mr = 56965 m= 4610 mr = 22241 m= 271 mr = 3022 m= 0 mr = 108 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 1014 time to turn everything in is 0.8100000 number of dielectric boundary points 32268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 20400 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) : 0.6355327 object centre at (A) : 19.67200 8.008501 14.85700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1193964E-02 -6.3036510E-05 midg,1,midg; midg,igrid,midg 1.6683111E-02 1.3866196E-02 1,midg,midg; igrid,midg,midg 7.1954221E-02 -2.5690211E-02 gauss-seidel spectral radius is 0.9986488 estimated iterations to convergence 216 setup time was (sec) 1.140000 now iterating at: 22:45:53 rms-change max change #iterations 4.458081 196.6180 at 10iterations 2.087601 65.54671 at 20iterations 0.9854530 29.55375 at 30iterations 0.4646022 14.56150 at 40iterations 0.2183225 7.371542 at 50iterations 0.1030253 3.038454 at 60iterations 4.8614278E-02 1.536381 at 70iterations 2.2854868E-02 0.7089987 at 80iterations 1.0943578E-02 0.3254089 at 90iterations 5.2709966E-03 0.2031155 at 100iterations 2.5896132E-03 9.1741085E-02 at 110iterations 1.3224793E-03 5.0033569E-02 at 120iterations finished qdiffx linear iterations at : 22:46:02 total time elapsed so far: 10.09000 # loops : 120 mean,max change (kT/e) : 1.3224793E-03 5.0033569E-02 energy calculations done at 10.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.30000 DelPhi exited at 22:46:03 10.309u 0.445s 0:11.14 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 Mon Oct 10 2011 at 22:46:03 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2746 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.859897 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): -8.335999 47.68000 ymin,ymax (A): -15.45100 31.46800 zmin,zma (A): -11.82000 41.53400 x,y,z range (A): 56.01600 46.91900 53.35400 scale (grids/A): 2.859897 object centre (A): 19.67200 8.008501 14.85700 number of atom coordinates read : 2746 total number of charged atoms : 2595 net assigned charge : 5.312014 assigned positive charge : 416.1705 centred at (gu) : 87.53634 89.50650 85.88129 assigned negative charge : -410.8593 centred at (gu) : 88.82579 89.51143 86.10173 start vw surface at 0.1700000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 186112 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22574 grid for indexing accessible points = 1.400000 m= 94963 mr = 137701 m= 34435 mr = 79072 m= 8563 mr = 28299 m= 1264 mr = 6686 m= 76 mr = 879 m= 0 mr = 39 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 3514 time to turn everything in is 2.150000 number of dielectric boundary points 72737 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.300000 number of grid points assigned charge 20760 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) : 1.906598 object centre at (A) : 19.67200 8.008501 14.85700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1886509 -7.0701815E-02 midg,1,midg; midg,igrid,midg 0.2384742 0.1465457 1,midg,midg; igrid,midg,midg 0.7513415 -0.2982902 gauss-seidel spectral radius is 0.9992570 estimated iterations to convergence 290 setup time was (sec) 2.510000 now iterating at: 22:46:06 rms-change max change #iterations 10.29534 375.6391 at 10iterations 5.952762 141.7280 at 20iterations 3.438562 62.58508 at 30iterations 1.983106 41.14105 at 40iterations 1.140472 24.31379 at 50iterations 0.6560835 11.77419 at 60iterations 0.3758250 7.419067 at 70iterations 0.2170645 3.832635 at 80iterations 0.1243172 2.307528 at 90iterations 7.1486622E-02 1.445168 at 100iterations 4.1033417E-02 0.7087593 at 110iterations 2.3614448E-02 0.4249725 at 120iterations 1.3636856E-02 0.2470398 at 130iterations 7.9020774E-03 0.1483994 at 140iterations 4.6238634E-03 8.1775665E-02 at 150iterations 2.7486344E-03 6.0178757E-02 at 160iterations 1.6790713E-03 3.8551331E-02 at 170iterations 1.0701814E-03 2.5871277E-02 at 180iterations finished qdiffx linear iterations at : 22:46:21 total time elapsed so far: 17.49000 # loops : 180 mean,max change (kT/e) : 1.0701814E-03 2.5871277E-02 energy calculations done at 17.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.70000 DelPhi exited at 22:46:21 17.707u 0.488s 0:18.51 98.2% 0+0k 0+0io 0pf+0w