Mon Oct 10 17:05:51 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 17:05:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2735 !!! WARNING: ALA 182 has a net charge of -0.0570 !!! WARNING: ASN 312 has a net charge of -0.0550 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: 0.6127894 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): -32.67200 23.11800 ymin,ymax (A): 40.24900 89.85900 zmin,zma (A): 0.3490000 58.44400 x,y,z range (A): 55.79000 49.61000 58.09500 scale (grids/A): 0.6127894 object centre (A): -4.777000 65.05400 29.39650 number of atom coordinates read : 2735 total number of charged atoms : 2595 net assigned charge : 3.388016 assigned positive charge : 409.4975 centred at (gu) : 91.88035 89.49191 89.12459 assigned negative charge : -406.1102 centred at (gu) : 91.84444 89.52943 89.18046 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6933 nv = 96 ne = 84 npr = 54537 no. pairs analyzed = 54537 no. exposed pairs = 3682 no. arc points = 25526 no. surface atoms = 1241 nbur = 1494 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 352 mr = 3664 m= 0 mr = 20 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2557 ## 275 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8539 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3199570E-09 -8.5296792E-10 midg,1,midg; midg,igrid,midg 4.6793009E-09 -8.9066844E-12 1,midg,midg; igrid,midg,midg 7.6168169E-11 6.2261645E-09 gauss-seidel spectral radius is 0.9862312 estimated iterations to convergence 70 setup time was (sec) 0.6300000 now iterating at: 17:05:52 rms-change max change #iterations 0.1229757 16.80806 at 10iterations 1.0913547E-02 1.806263 at 20iterations 9.9062361E-04 0.1509094 at 30iterations 9.4117873E-05 1.3165474E-02 at 40iterations 1.0813439E-05 1.6441345E-03 at 50iterations finished qdiffx linear iterations at : 17:05:56 total time elapsed so far: 4.980000 # loops : 50 mean,max change (kT/e) : 1.0813439E-05 1.6441345E-03 energy calculations done at 4.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.150000 DelPhi exited at 17:05:57 5.156u 0.459s 0:06.00 93.3% 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 17:05:57 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 = 2735 !!! WARNING: ALA 182 has a net charge of -0.0570 !!! WARNING: ASN 312 has a net charge of -0.0550 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: 1.838368 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): -32.67200 23.11800 ymin,ymax (A): 40.24900 89.85900 zmin,zma (A): 0.3490000 58.44400 x,y,z range (A): 55.79000 49.61000 58.09500 scale (grids/A): 1.838368 object centre (A): -4.777000 65.05400 29.39650 number of atom coordinates read : 2735 total number of charged atoms : 2595 net assigned charge : 3.388016 assigned positive charge : 409.4975 centred at (gu) : 95.64071 88.47505 87.37308 assigned negative charge : -406.1102 centred at (gu) : 95.53290 88.58801 87.54082 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25526 grid for indexing accessible points = 1.400000 m= 25470 mr = 50583 m= 3542 mr = 18219 m= 138 mr = 2016 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 730 time to turn everything in is 0.6300000 number of dielectric boundary points 33360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20291 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) : 0.6127894 object centre at (A) : -4.777000 65.05400 29.39650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3997592E-02 -5.1421590E-02 midg,1,midg; midg,igrid,midg 1.0654327E-02 6.0454849E-03 1,midg,midg; igrid,midg,midg -4.1339267E-03 8.7747537E-03 gauss-seidel spectral radius is 0.9985610 estimated iterations to convergence 209 setup time was (sec) 1.030000 now iterating at: 17:05:58 rms-change max change #iterations 4.053236 184.2126 at 10iterations 1.856253 63.37587 at 20iterations 0.8507397 29.31705 at 30iterations 0.3903450 12.22076 at 40iterations 0.1781043 6.590034 at 50iterations 8.1866316E-02 2.634746 at 60iterations 3.7545547E-02 1.206854 at 70iterations 1.7264010E-02 0.5884943 at 80iterations 7.9120388E-03 0.2726212 at 90iterations 3.6444757E-03 0.1154099 at 100iterations 1.6737579E-03 5.3226233E-02 at 110iterations 7.6940109E-04 2.4239540E-02 at 120iterations finished qdiffx linear iterations at : 17:06:09 total time elapsed so far: 12.12000 # loops : 120 mean,max change (kT/e) : 7.6940109E-04 2.4239540E-02 energy calculations done at 12.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 17:06:10 12.300u 0.513s 0:13.35 95.9% 0+0k 0+0io 3pf+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 17:06:10 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 = 2735 !!! WARNING: ALA 182 has a net charge of -0.0570 !!! WARNING: ASN 312 has a net charge of -0.0550 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: 2.757552 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): -32.67200 23.11800 ymin,ymax (A): 40.24900 89.85900 zmin,zma (A): 0.3490000 58.44400 x,y,z range (A): 55.79000 49.61000 58.09500 scale (grids/A): 2.757552 object centre (A): -4.777000 65.05400 29.39650 number of atom coordinates read : 2735 total number of charged atoms : 2595 net assigned charge : 3.388016 assigned positive charge : 409.4975 centred at (gu) : 98.46078 87.71229 86.05927 assigned negative charge : -406.1102 centred at (gu) : 98.29929 87.88203 86.31121 start vw surface at 0.1200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 173734 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25526 grid for indexing accessible points = 1.400000 m= 84194 mr = 123260 m= 28294 mr = 67547 m= 6172 mr = 22196 m= 656 mr = 4443 m= 19 mr = 335 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 2491 time to turn everything in is 1.610000 number of dielectric boundary points 75288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 20757 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) : 1.838368 object centre at (A) : -4.777000 65.05400 29.39650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4354727 -0.9836373 midg,1,midg; midg,igrid,midg 8.1478521E-02 3.1942610E-02 1,midg,midg; igrid,midg,midg -2.5470699E-03 9.4133154E-02 gauss-seidel spectral radius is 0.9992524 estimated iterations to convergence 289 setup time was (sec) 1.980000 now iterating at: 17:06:13 rms-change max change #iterations 9.790120 339.5220 at 10iterations 5.743728 151.9186 at 20iterations 3.359512 70.53779 at 30iterations 1.947191 47.64618 at 40iterations 1.129442 22.24079 at 50iterations 0.6518793 13.52233 at 60iterations 0.3748166 7.474276 at 70iterations 0.2163301 4.279305 at 80iterations 0.1242794 2.369924 at 90iterations 7.1584642E-02 1.315998 at 100iterations 4.0999815E-02 0.7723446 at 110iterations 2.3536928E-02 0.4334602 at 120iterations 1.3506602E-02 0.2689381 at 130iterations 7.7465861E-03 0.1367788 at 140iterations 4.4426452E-03 8.5638046E-02 at 150iterations 2.5441640E-03 4.5935631E-02 at 160iterations 1.4566104E-03 2.5308609E-02 at 170iterations 8.3602982E-04 1.4019012E-02 at 180iterations finished qdiffx linear iterations at : 17:06:31 total time elapsed so far: 20.30000 # loops : 180 mean,max change (kT/e) : 8.3602982E-04 1.4019012E-02 energy calculations done at 20.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.47000 DelPhi exited at 17:06:32 20.475u 0.566s 0:21.66 97.0% 0+0k 0+0io 0pf+0w