Sat Oct 8 11:36:37 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 Sat Oct 8 2011 at 11:36:37 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 = 4490 !!! WARNING: GLM 74 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5168108 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): -55.68800 13.19600 ymin,ymax (A): 73.04800 136.4720 zmin,zma (A): 4.246000 62.38900 x,y,z range (A): 68.88400 63.42400 58.14300 scale (grids/A): 0.5168108 object centre (A): -21.24600 104.7600 33.31750 number of atom coordinates read : 4490 total number of charged atoms : 4326 net assigned charge : -4.593951 assigned positive charge : 677.0009 centred at (gu) : 88.99980 88.21233 90.26720 assigned negative charge : -681.5983 centred at (gu) : 88.99218 88.33499 90.46413 start vw surface at 0.2300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 7378 nv = 96 ne = 84 npr = 94084 no. pairs analyzed = 94084 no. exposed pairs = 5094 no. arc points = 34507 no. surface atoms = 1732 nbur = 2758 mkacc time = 0.3100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 265 mr = 4138 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.6200000 number of dielectric boundary points 3494 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3459 ## 533 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 10060 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8858140E-10 -7.9160029E-10 midg,1,midg; midg,igrid,midg 4.8107113E-10 -3.0750358E-10 1,midg,midg; igrid,midg,midg -1.4822393E-10 -5.1288286E-11 gauss-seidel spectral radius is 0.9808182 estimated iterations to convergence 60 setup time was (sec) 0.9200000 now iterating at: 11:36:38 rms-change max change #iterations 7.0445769E-02 13.09680 at 10iterations 4.3494431E-03 0.7668800 at 20iterations 5.2079646E-04 7.3616028E-02 at 30iterations 1.4889921E-04 2.1870017E-02 at 40iterations 5.3095748E-05 8.6760521E-03 at 50iterations finished qdiffx linear iterations at : 11:36:42 total time elapsed so far: 4.920000 # loops : 50 mean,max change (kT/e) : 5.3095748E-05 8.6760521E-03 energy calculations done at 4.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.130000 DelPhi exited at 11:36:43 5.136u 0.454s 0:06.08 91.7% 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 Sat Oct 8 2011 at 11:36:43 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4490 !!! WARNING: GLM 74 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.550433 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): -55.68800 13.19600 ymin,ymax (A): 73.04800 136.4720 zmin,zma (A): 4.246000 62.38900 x,y,z range (A): 68.88400 63.42400 58.14300 scale (grids/A): 1.550433 object centre (A): -21.24600 104.7600 33.31750 number of atom coordinates read : 4490 total number of charged atoms : 4326 net assigned charge : -4.593951 assigned positive charge : 677.0009 centred at (gu) : 86.99802 84.63563 90.80030 assigned negative charge : -681.5983 centred at (gu) : 86.97604 85.00473 91.39187 start vw surface at 0.2400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 83814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34507 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 25609 mr = 59734 m= 2348 mr = 18138 m= 45 mr = 1212 m= 0 mr = 2 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 4723 time to turn everything in is 0.9000000 number of dielectric boundary points 32730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 493 ## 7 charges are in solution ## iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 32592 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) : 0.5168108 object centre at (A) : -21.24600 104.7600 33.31750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8186536E-02 -1.5504870E-02 midg,1,midg; midg,igrid,midg 1.4493897E-02 -1.7482683E-02 1,midg,midg; igrid,midg,midg -2.2171205E-02 -7.8291725E-03 gauss-seidel spectral radius is 0.9981124 estimated iterations to convergence 183 setup time was (sec) 1.250000 now iterating at: 11:36:45 rms-change max change #iterations 3.760648 177.3967 at 10iterations 1.539168 52.35180 at 20iterations 0.6330402 19.54392 at 30iterations 0.2603637 8.259087 at 40iterations 0.1070574 3.420242 at 50iterations 4.3956570E-02 1.541866 at 60iterations 1.8131467E-02 0.6130753 at 70iterations 7.4752732E-03 0.2450514 at 80iterations 3.1169516E-03 9.9906921E-02 at 90iterations 1.3239107E-03 4.4477224E-02 at 100iterations 5.8925437E-04 2.3595810E-02 at 110iterations 2.8815531E-04 1.0389328E-02 at 120iterations finished qdiffx linear iterations at : 11:36:55 total time elapsed so far: 11.33000 # loops : 120 mean,max change (kT/e) : 2.8815531E-04 1.0389328E-02 energy calculations done at 11.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 11:36:55 11.565u 0.485s 0:12.40 97.0% 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 Sat Oct 8 2011 at 11:36:55 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 = 4490 !!! WARNING: GLM 74 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.325649 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): -55.68800 13.19600 ymin,ymax (A): 73.04800 136.4720 zmin,zma (A): 4.246000 62.38900 x,y,z range (A): 68.88400 63.42400 58.14300 scale (grids/A): 2.325649 object centre (A): -21.24600 104.7600 33.31750 number of atom coordinates read : 4490 total number of charged atoms : 4326 net assigned charge : -4.593951 assigned positive charge : 677.0009 centred at (gu) : 85.49663 81.95311 91.20004 assigned negative charge : -681.5983 centred at (gu) : 85.46404 82.50700 92.08781 start vw surface at 0.2200000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 195581 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34507 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 90582 mr = 146155 m= 24419 mr = 73038 m= 3526 mr = 18868 m= 150 mr = 2340 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 15505 time to turn everything in is 2.120000 number of dielectric boundary points 73802 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 2.300000 number of grid points assigned charge 34516 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) : 1.550433 object centre at (A) : -21.24600 104.7600 33.31750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3148143 -0.2718089 midg,1,midg; midg,igrid,midg 0.2945848 -0.3913482 1,midg,midg; igrid,midg,midg -0.6754734 -3.7577324E-02 gauss-seidel spectral radius is 0.9991407 estimated iterations to convergence 269 setup time was (sec) 2.520000 now iterating at: 11:36:58 rms-change max change #iterations 9.976892 270.3096 at 10iterations 5.625789 128.1713 at 20iterations 3.147147 71.83678 at 30iterations 1.753551 36.18852 at 40iterations 0.9772654 19.67279 at 50iterations 0.5418005 14.48631 at 60iterations 0.2998036 5.807200 at 70iterations 0.1657996 3.538225 at 80iterations 9.1628611E-02 1.698584 at 90iterations 5.0541684E-02 0.9546280 at 100iterations 2.7928542E-02 0.5445290 at 110iterations 1.5382472E-02 0.2882271 at 120iterations 8.4932614E-03 0.1557665 at 130iterations 4.6966155E-03 8.3927155E-02 at 140iterations 2.6035439E-03 6.2053680E-02 at 150iterations 1.4504265E-03 2.8142452E-02 at 160iterations 8.1811787E-04 1.4496326E-02 at 170iterations 4.7096054E-04 8.7623596E-03 at 180iterations finished qdiffx linear iterations at : 11:37:15 total time elapsed so far: 19.57000 # loops : 180 mean,max change (kT/e) : 4.7096054E-04 8.7623596E-03 energy calculations done at 19.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.79000 DelPhi exited at 11:37:16 19.797u 0.533s 0:20.65 98.4% 0+0k 0+0io 0pf+0w