Wed Nov 9 16:01:27 PST 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 Wed Nov 9 2011 at 16:01:27 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1065 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3242 !!! WARNING: UMP 529 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5870809 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): 0.7670001 49.12500 ymin,ymax (A): -7.560000 48.96000 zmin,zma (A): 0.8219999 61.46100 x,y,z range (A): 48.35800 56.52000 60.63900 scale (grids/A): 0.5870809 object centre (A): 24.94600 20.70000 31.14150 number of atom coordinates read : 3242 total number of charged atoms : 3099 net assigned charge : -7.999967 assigned positive charge : 489.4817 centred at (gu) : 89.54828 89.23162 90.79163 assigned negative charge : -497.4830 centred at (gu) : 89.42342 89.13424 90.75637 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7447 nv = 96 ne = 84 npr = 66683 no. pairs analyzed = 66683 no. exposed pairs = 3736 no. arc points = 25641 no. surface atoms = 1285 nbur = 1957 mkacc time = 0.1300000 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 = 1.456000 m= 321 mr = 4307 m= 1 mr = 35 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 0.2800000 number of dielectric boundary points 3427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2674 ## 267 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 9333 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7460780E-09 -1.2990474E-09 midg,1,midg; midg,igrid,midg -6.2678209E-09 6.5154215E-10 1,midg,midg; igrid,midg,midg -6.7968737E-09 1.4560733E-09 gauss-seidel spectral radius is 0.9850369 estimated iterations to convergence 67 setup time was (sec) 0.4900000 now iterating at: 16:01:28 rms-change max change #iterations 0.1120206 16.29309 at 10iterations 9.1346195E-03 1.280783 at 20iterations 7.4467494E-04 9.7824097E-02 at 30iterations 6.0742805E-05 8.0561638E-03 at 40iterations 5.0223011E-06 7.1907043E-04 at 50iterations finished qdiffx linear iterations at : 16:01:31 total time elapsed so far: 3.810000 # loops : 50 mean,max change (kT/e) : 5.0223011E-06 7.1907043E-04 energy calculations done at 3.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.960000 DelPhi exited at 16:01:32 3.964u 0.178s 0:04.92 83.9% 0+0k 0+45976io 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 Wed Nov 9 2011 at 16:01:32 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1065 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3242 !!! WARNING: UMP 529 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: 1.761243 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): 0.7670001 49.12500 ymin,ymax (A): -7.560000 48.96000 zmin,zma (A): 0.8219999 61.46100 x,y,z range (A): 48.35800 56.52000 60.63900 scale (grids/A): 1.761243 object centre (A): 24.94600 20.70000 31.14150 number of atom coordinates read : 3242 total number of charged atoms : 3099 net assigned charge : -7.999967 assigned positive charge : 489.4817 centred at (gu) : 88.64416 87.69408 92.37370 assigned negative charge : -497.4830 centred at (gu) : 88.26987 87.40237 92.26873 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 81505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25641 grid for indexing accessible points = 1.400000 m= 29334 mr = 58853 m= 3902 mr = 22267 m= 137 mr = 2268 m= 0 mr = 26 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 960 time to turn everything in is 0.5000000 number of dielectric boundary points 31464 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 211 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 24117 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) : 0.5870809 object centre at (A) : 24.94600 20.70000 31.14150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4593299E-02 -1.3741170E-02 midg,1,midg; midg,igrid,midg -3.3780526E-02 4.9752498E-04 1,midg,midg; igrid,midg,midg -2.5411688E-02 7.5282273E-03 gauss-seidel spectral radius is 0.9984681 estimated iterations to convergence 203 setup time was (sec) 0.7100000 now iterating at: 16:01:33 rms-change max change #iterations 4.159275 161.3182 at 10iterations 1.852895 57.71112 at 20iterations 0.8321621 27.44423 at 30iterations 0.3723105 11.21992 at 40iterations 0.1671713 5.525722 at 50iterations 7.4981831E-02 2.555851 at 60iterations 3.3707529E-02 1.149180 at 70iterations 1.5083166E-02 0.4471040 at 80iterations 6.7891963E-03 0.2159004 at 90iterations 3.0505005E-03 9.3830109E-02 at 100iterations 1.3706932E-03 4.6798680E-02 at 110iterations 6.1706011E-04 2.0746231E-02 at 120iterations finished qdiffx linear iterations at : 16:01:41 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 6.1706011E-04 2.0746231E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 16:01:41 8.106u 0.211s 0:08.88 93.5% 0+0k 0+45352io 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 Wed Nov 9 2011 at 16:01:41 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1065 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3242 !!! WARNING: UMP 529 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.641864 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): 0.7670001 49.12500 ymin,ymax (A): -7.560000 48.96000 zmin,zma (A): 0.8219999 61.46100 x,y,z range (A): 48.35800 56.52000 60.63900 scale (grids/A): 2.641864 object centre (A): 24.94600 20.70000 31.14150 number of atom coordinates read : 3242 total number of charged atoms : 3099 net assigned charge : -7.999967 assigned positive charge : 489.4817 centred at (gu) : 87.96605 86.54096 93.56046 assigned negative charge : -497.4830 centred at (gu) : 87.40466 86.10333 93.40302 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 188877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25641 grid for indexing accessible points = 1.400000 m= 97683 mr = 142435 m= 33239 mr = 81452 m= 6690 mr = 26934 m= 690 mr = 4928 m= 22 mr = 397 m= 0 mr = 5 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 3792 time to turn everything in is 1.280000 number of dielectric boundary points 71050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 24783 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) : 1.761243 object centre at (A) : 24.94600 20.70000 31.14150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3634129 -0.4510346 midg,1,midg; midg,igrid,midg -0.5487540 -9.9322628E-03 1,midg,midg; igrid,midg,midg -0.2867268 0.1155068 gauss-seidel spectral radius is 0.9992200 estimated iterations to convergence 283 setup time was (sec) 1.510000 now iterating at: 16:01:43 rms-change max change #iterations 10.15206 247.6201 at 10iterations 5.843941 155.8435 at 20iterations 3.357350 79.47528 at 30iterations 1.919075 40.65410 at 40iterations 1.095723 20.62564 at 50iterations 0.6228844 10.82039 at 60iterations 0.3542028 6.818668 at 70iterations 0.2013314 3.682810 at 80iterations 0.1143015 2.264618 at 90iterations 6.4947069E-02 1.136410 at 100iterations 3.6708284E-02 0.6652222 at 110iterations 2.0827364E-02 0.3794603 at 120iterations 1.1828723E-02 0.2037811 at 130iterations 6.6875131E-03 0.1152935 at 140iterations 3.7909227E-03 6.8429947E-02 at 150iterations 2.1519826E-03 3.9762974E-02 at 160iterations 1.2200385E-03 2.1419525E-02 at 170iterations 6.9416728E-04 1.3516903E-02 at 180iterations finished qdiffx linear iterations at : 16:01:54 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 6.9416728E-04 1.3516903E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 16:01:55 13.101u 0.225s 0:13.76 96.8% 0+0k 0+45344io 0pf+0w