Tue Oct 11 06:16:12 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 Tue Oct 11 2011 at 06:16:12 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2109 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 192 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6839051 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): 15.80200 62.55700 ymin,ymax (A): -3.533000 33.73700 zmin,zma (A): 19.93700 71.99100 x,y,z range (A): 46.75500 37.27000 52.05400 scale (grids/A): 0.6839051 object centre (A): 39.17950 15.10200 45.96400 number of atom coordinates read : 2109 total number of charged atoms : 1977 net assigned charge : 6.420009 assigned positive charge : 322.0659 centred at (gu) : 91.51099 89.66104 89.23629 assigned negative charge : -315.6461 centred at (gu) : 91.63806 89.68852 89.15942 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6635 nv = 96 ne = 84 npr = 42233 no. pairs analyzed = 42233 no. exposed pairs = 2561 no. arc points = 17434 no. surface atoms = 870 nbur = 1239 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 393 mr = 3797 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1707 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7551 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9488009E-09 4.5825633E-08 midg,1,midg; midg,igrid,midg 4.1858272E-08 2.1786693E-08 1,midg,midg; igrid,midg,midg 5.0039358E-08 -9.0783185E-09 gauss-seidel spectral radius is 0.9888641 estimated iterations to convergence 77 setup time was (sec) 0.5600000 now iterating at: 06:16:12 rms-change max change #iterations 0.1777621 28.09697 at 10iterations 2.0669281E-02 2.891407 at 20iterations 2.6246051E-03 0.3641472 at 30iterations 4.3059365E-04 6.5467834E-02 at 40iterations 1.1497687E-04 1.6736984E-02 at 50iterations finished qdiffx linear iterations at : 06:16:16 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 1.1497687E-04 1.6736984E-02 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 06:16:16 4.005u 0.269s 0:04.61 92.4% 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 Tue Oct 11 2011 at 06:16:16 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2109 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 192 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.051715 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): 15.80200 62.55700 ymin,ymax (A): -3.533000 33.73700 zmin,zma (A): 19.93700 71.99100 x,y,z range (A): 46.75500 37.27000 52.05400 scale (grids/A): 2.051715 object centre (A): 39.17950 15.10200 45.96400 number of atom coordinates read : 2109 total number of charged atoms : 1977 net assigned charge : 6.420009 assigned positive charge : 322.0659 centred at (gu) : 94.53302 88.98316 87.70881 assigned negative charge : -315.6461 centred at (gu) : 94.91405 89.06572 87.47830 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 70961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17434 grid for indexing accessible points = 1.400000 m= 27901 mr = 50453 m= 4902 mr = 20965 m= 387 mr = 3196 m= 7 mr = 212 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 29332 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 15647 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) : 0.6839051 object centre at (A) : 39.17950 15.10200 45.96400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7127655E-02 4.7013078E-02 midg,1,midg; midg,igrid,midg 2.3201268E-02 1.0063896E-02 1,midg,midg; igrid,midg,midg 2.2369353E-02 1.2890588E-02 gauss-seidel spectral radius is 0.9987602 estimated iterations to convergence 225 setup time was (sec) 0.9300000 now iterating at: 06:16:18 rms-change max change #iterations 4.371802 205.4697 at 10iterations 2.129100 78.95602 at 20iterations 1.029934 37.80442 at 30iterations 0.5017775 15.18786 at 40iterations 0.2449983 7.534348 at 50iterations 0.1187803 3.617420 at 60iterations 5.7980854E-02 1.823752 at 70iterations 2.8316004E-02 0.9180040 at 80iterations 1.3830520E-02 0.4412365 at 90iterations 6.7780898E-03 0.1933441 at 100iterations 3.3690741E-03 0.1200123 at 110iterations 1.7078605E-03 5.6262970E-02 at 120iterations finished qdiffx linear iterations at : 06:16:26 total time elapsed so far: 9.150000 # loops : 120 mean,max change (kT/e) : 1.7078605E-03 5.6262970E-02 energy calculations done at 9.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 06:16:27 9.322u 0.321s 0:10.18 94.6% 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 06:16:27 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2109 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 192 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.077573 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): 15.80200 62.55700 ymin,ymax (A): -3.533000 33.73700 zmin,zma (A): 19.93700 71.99100 x,y,z range (A): 46.75500 37.27000 52.05400 scale (grids/A): 3.077573 object centre (A): 39.17950 15.10200 45.96400 number of atom coordinates read : 2109 total number of charged atoms : 1977 net assigned charge : 6.420009 assigned positive charge : 322.0659 centred at (gu) : 96.79935 88.47473 86.56319 assigned negative charge : -315.6461 centred at (gu) : 97.37101 88.59850 86.21750 start vw surface at 0.1300000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 163482 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17434 grid for indexing accessible points = 1.400000 m= 88113 mr = 121204 m= 34274 mr = 73237 m= 9072 mr = 27929 m= 1667 mr = 6981 m= 166 mr = 1234 m= 6 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.060000 number of dielectric boundary points 66100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.210000 number of grid points assigned charge 15811 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) : 2.051715 object centre at (A) : 39.17950 15.10200 45.96400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2416829 0.3560152 midg,1,midg; midg,igrid,midg 0.2160226 7.4168228E-02 1,midg,midg; igrid,midg,midg 0.1964996 0.3620309 gauss-seidel spectral radius is 0.9992801 estimated iterations to convergence 294 setup time was (sec) 2.380000 now iterating at: 06:16:29 rms-change max change #iterations 9.926116 389.5922 at 10iterations 5.831593 122.2598 at 20iterations 3.423727 70.85838 at 30iterations 2.011657 41.81278 at 40iterations 1.178509 24.49213 at 50iterations 0.6874303 14.02847 at 60iterations 0.4013227 7.591389 at 70iterations 0.2337218 4.256450 at 80iterations 0.1365511 2.626505 at 90iterations 7.9442404E-02 1.575793 at 100iterations 4.6382491E-02 0.8656807 at 110iterations 2.7087796E-02 0.5206718 at 120iterations 1.5909079E-02 0.2851667 at 130iterations 9.4362851E-03 0.1842499 at 140iterations 5.6808302E-03 0.1044054 at 150iterations 3.5229716E-03 6.4957321E-02 at 160iterations 2.2883930E-03 4.3979645E-02 at 170iterations 1.5720408E-03 3.0942917E-02 at 180iterations finished qdiffx linear iterations at : 06:16:43 total time elapsed so far: 15.85000 # loops : 180 mean,max change (kT/e) : 1.5720408E-03 3.0942917E-02 energy calculations done at 15.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.03000 DelPhi exited at 06:16:43 16.032u 0.304s 0:16.62 98.2% 0+0k 0+0io 0pf+0w