Sat Oct 15 13:05:22 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 Sat Oct 15 2011 at 13:05:22 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 = 3691 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: 0.4962364 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): -19.45300 40.87400 ymin,ymax (A): -20.60400 34.30100 zmin,zma (A): -13.81700 57.92300 x,y,z range (A): 60.32700 54.90500 71.74000 scale (grids/A): 0.4962364 object centre (A): 10.71050 6.848501 22.05300 number of atom coordinates read : 3691 total number of charged atoms : 3541 net assigned charge : 5.500020 assigned positive charge : 567.2681 centred at (gu) : 89.42360 89.33329 90.72081 assigned negative charge : -561.7708 centred at (gu) : 89.34206 89.30090 90.68131 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5723 nv = 96 ne = 84 npr = 70584 no. pairs analyzed = 70584 no. exposed pairs = 4977 no. arc points = 35791 no. surface atoms = 1671 nbur = 2020 mkacc time = 0.1200000 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 = 1.708000 m= 186 mr = 2641 m= 0 mr = 4 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3508 ## 664 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 7781 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5034018E-12 1.0139491E-10 midg,1,midg; midg,igrid,midg 6.3622922E-12 6.3435229E-11 1,midg,midg; igrid,midg,midg -5.7182141E-11 1.0977195E-10 gauss-seidel spectral radius is 0.9791711 estimated iterations to convergence 57 setup time was (sec) 0.4400000 now iterating at: 13:05:22 rms-change max change #iterations 4.8985742E-02 9.447571 at 10iterations 2.9611958E-03 0.5331993 at 20iterations 3.7945932E-04 0.1026611 at 30iterations 7.8204816E-05 2.0526886E-02 at 40iterations 1.6991688E-05 4.3678284E-03 at 50iterations finished qdiffx linear iterations at : 13:05:25 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 1.6991688E-05 4.3678284E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 13:05:26 3.587u 0.191s 0:04.11 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 15 2011 at 13:05:26 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 = 3691 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: 1.488709 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): -19.45300 40.87400 ymin,ymax (A): -20.60400 34.30100 zmin,zma (A): -13.81700 57.92300 x,y,z range (A): 60.32700 54.90500 71.74000 scale (grids/A): 1.488709 object centre (A): 10.71050 6.848501 22.05300 number of atom coordinates read : 3691 total number of charged atoms : 3541 net assigned charge : 5.500020 assigned positive charge : 567.2681 centred at (gu) : 88.26984 87.99869 92.16115 assigned negative charge : -561.7708 centred at (gu) : 88.02582 87.90246 92.04350 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64600 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35791 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 15874 mr = 40971 m= 1121 mr = 9528 m= 20 mr = 380 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 98 time to turn everything in is 0.3200000 number of dielectric boundary points 30736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 655 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 26292 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) : 0.4962364 object centre at (A) : 10.71050 6.848501 22.05300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7890227E-03 9.3566217E-03 midg,1,midg; midg,igrid,midg 2.3592790E-03 2.2310494E-03 1,midg,midg; igrid,midg,midg -2.9558185E-03 1.8968137E-03 gauss-seidel spectral radius is 0.9978740 estimated iterations to convergence 173 setup time was (sec) 0.5500000 now iterating at: 13:05:27 rms-change max change #iterations 3.050979 176.7548 at 10iterations 1.174614 48.34221 at 20iterations 0.4556841 18.95563 at 30iterations 0.1769399 6.343201 at 40iterations 6.8502992E-02 2.791498 at 50iterations 2.6692489E-02 0.9815121 at 60iterations 1.0473024E-02 0.3871346 at 70iterations 4.1139019E-03 0.1700249 at 80iterations 1.6522235E-03 6.4173698E-02 at 90iterations 6.9031009E-04 2.8896332E-02 at 100iterations 3.0365991E-04 1.4648438E-02 at 110iterations 1.4408963E-04 6.9465637E-03 at 120iterations finished qdiffx linear iterations at : 13:05:34 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 1.4408963E-04 6.9465637E-03 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 13:05:34 7.987u 0.219s 0:08.47 96.6% 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 Sat Oct 15 2011 at 13:05:34 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 = 3691 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: 2.233064 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): -19.45300 40.87400 ymin,ymax (A): -20.60400 34.30100 zmin,zma (A): -13.81700 57.92300 x,y,z range (A): 60.32700 54.90500 71.74000 scale (grids/A): 2.233064 object centre (A): 10.71050 6.848501 22.05300 number of atom coordinates read : 3691 total number of charged atoms : 3541 net assigned charge : 5.500020 assigned positive charge : 567.2681 centred at (gu) : 87.40427 86.99751 93.24155 assigned negative charge : -561.7708 centred at (gu) : 87.03867 86.85369 93.06517 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 150357 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35791 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 59310 mr = 101835 m= 12746 mr = 43623 m= 1515 mr = 8371 m= 58 mr = 787 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 308 time to turn everything in is 0.7600000 number of dielectric boundary points 69363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 28207 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) : 1.488709 object centre at (A) : 10.71050 6.848501 22.05300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4754457E-02 0.2583714 midg,1,midg; midg,igrid,midg 4.2459264E-02 3.0012535E-02 1,midg,midg; igrid,midg,midg -3.9075382E-02 1.4937573E-02 gauss-seidel spectral radius is 0.9990618 estimated iterations to convergence 258 setup time was (sec) 1.010000 now iterating at: 13:05:36 rms-change max change #iterations 8.635855 258.0097 at 10iterations 4.815979 141.6263 at 20iterations 2.669309 66.98621 at 30iterations 1.461115 38.24600 at 40iterations 0.7977045 19.45881 at 50iterations 0.4340141 11.06027 at 60iterations 0.2353555 5.727085 at 70iterations 0.1273984 2.838360 at 80iterations 6.8692341E-02 1.593231 at 90iterations 3.7104968E-02 0.8850555 at 100iterations 1.9968769E-02 0.4454880 at 110iterations 1.0740279E-02 0.2413824 at 120iterations 5.7867230E-03 0.1315155 at 130iterations 3.1288192E-03 7.5073242E-02 at 140iterations 1.6942810E-03 4.2997718E-02 at 150iterations 9.1932283E-04 2.1789551E-02 at 160iterations 5.0443591E-04 1.3109207E-02 at 170iterations 2.8200087E-04 7.6675415E-03 at 180iterations finished qdiffx linear iterations at : 13:05:47 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 2.8200087E-04 7.6675415E-03 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 13:05:48 12.860u 0.237s 0:13.46 97.2% 0+0k 0+0io 0pf+0w