Tue Oct 11 04:18:02 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 04:18:03 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6613536 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): -14.88100 33.00600 ymin,ymax (A): 7.513999 55.95500 zmin,zma (A): 25.63000 79.45900 x,y,z range (A): 47.88700 48.44100 53.82900 scale (grids/A): 0.6613536 object centre (A): 9.062500 31.73450 52.54450 number of atom coordinates read : 2750 total number of charged atoms : 2598 net assigned charge : 4.154017 assigned positive charge : 419.3978 centred at (gu) : 90.07962 90.43510 88.58352 assigned negative charge : -415.2443 centred at (gu) : 90.37212 90.23727 88.61034 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8018 nv = 96 ne = 84 npr = 56589 no. pairs analyzed = 56589 no. exposed pairs = 3329 no. arc points = 23022 no. surface atoms = 1121 nbur = 1629 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 4608 m= 4 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.3000000 number of dielectric boundary points 3819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2251 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9517 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2341483E-08 3.8135766E-09 midg,1,midg; midg,igrid,midg -3.0372274E-08 5.8307787E-08 1,midg,midg; igrid,midg,midg 7.1670989E-08 -5.6127778E-08 gauss-seidel spectral radius is 0.9881595 estimated iterations to convergence 75 setup time was (sec) 0.5100000 now iterating at: 04:18:03 rms-change max change #iterations 0.1783084 23.47087 at 10iterations 1.9411348E-02 2.777550 at 20iterations 2.2174926E-03 0.3214626 at 30iterations 3.1271760E-04 4.3875694E-02 at 40iterations 6.8343361E-05 9.7312927E-03 at 50iterations finished qdiffx linear iterations at : 04:18:06 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 6.8343361E-05 9.7312927E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 04:18:06 3.115u 0.159s 0:03.69 88.3% 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 04:18:06 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.984061 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): -14.88100 33.00600 ymin,ymax (A): 7.513999 55.95500 zmin,zma (A): 25.63000 79.45900 x,y,z range (A): 47.88700 48.44100 53.82900 scale (grids/A): 1.984061 object centre (A): 9.062500 31.73450 52.54450 number of atom coordinates read : 2750 total number of charged atoms : 2598 net assigned charge : 4.154017 assigned positive charge : 419.3978 centred at (gu) : 90.23840 91.30496 85.75003 assigned negative charge : -415.2443 centred at (gu) : 91.11601 90.71159 85.83075 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 86828 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23022 grid for indexing accessible points = 1.400000 m= 32006 mr = 61835 m= 5111 mr = 23864 m= 300 mr = 3137 m= 3 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 436 time to turn everything in is 0.6000000 number of dielectric boundary points 35316 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 20520 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) : 0.6613536 object centre at (A) : 9.062500 31.73450 52.54450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8415816E-03 -1.5596428E-02 midg,1,midg; midg,igrid,midg -1.6181115E-02 4.3180067E-02 1,midg,midg; igrid,midg,midg 8.7963812E-02 -1.8915188E-02 gauss-seidel spectral radius is 0.9987497 estimated iterations to convergence 224 setup time was (sec) 0.8800000 now iterating at: 04:18:07 rms-change max change #iterations 4.860775 211.0286 at 10iterations 2.365857 83.79141 at 20iterations 1.143747 33.94148 at 30iterations 0.5548301 15.58556 at 40iterations 0.2697080 8.648594 at 50iterations 0.1304467 3.759153 at 60iterations 6.3244946E-02 2.058855 at 70iterations 3.0705692E-02 0.9610443 at 80iterations 1.4951067E-02 0.4101276 at 90iterations 7.2465315E-03 0.2073116 at 100iterations 3.5358465E-03 0.1102486 at 110iterations 1.7271114E-03 5.4550171E-02 at 120iterations finished qdiffx linear iterations at : 04:18:13 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 1.7271114E-03 5.4550171E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 04:18:14 6.998u 0.162s 0:07.68 93.0% 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 Tue Oct 11 2011 at 04:18:14 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.976091 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): -14.88100 33.00600 ymin,ymax (A): 7.513999 55.95500 zmin,zma (A): 25.63000 79.45900 x,y,z range (A): 47.88700 48.44100 53.82900 scale (grids/A): 2.976091 object centre (A): 9.062500 31.73450 52.54450 number of atom coordinates read : 2750 total number of charged atoms : 2598 net assigned charge : 4.154017 assigned positive charge : 419.3978 centred at (gu) : 90.35736 91.95729 83.62486 assigned negative charge : -415.2443 centred at (gu) : 91.67395 91.06727 83.74607 start vw surface at 0.1400000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 200445 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23022 grid for indexing accessible points = 1.400000 m= 103840 mr = 148854 m= 37466 mr = 85900 m= 8995 mr = 30191 m= 1375 mr = 6680 m= 109 mr = 910 m= 6 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 1491 time to turn everything in is 1.480000 number of dielectric boundary points 79660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 20780 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) : 1.984061 object centre at (A) : 9.062500 31.73450 52.54450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2148277 -0.1416930 midg,1,midg; midg,igrid,midg -0.1568400 0.4798732 1,midg,midg; igrid,midg,midg 0.7614932 -0.1070711 gauss-seidel spectral radius is 0.9992870 estimated iterations to convergence 295 setup time was (sec) 1.760000 now iterating at: 04:18:16 rms-change max change #iterations 11.07998 320.4348 at 10iterations 6.525593 142.1930 at 20iterations 3.828391 76.99446 at 30iterations 2.247563 54.38928 at 40iterations 1.314126 24.82739 at 50iterations 0.7696572 13.47297 at 60iterations 0.4486372 7.353572 at 70iterations 0.2621783 4.332024 at 80iterations 0.1528228 2.582929 at 90iterations 8.9197613E-02 1.448366 at 100iterations 5.2003771E-02 0.8821640 at 110iterations 3.0410273E-02 0.5225453 at 120iterations 1.7702905E-02 0.2943554 at 130iterations 1.0382728E-02 0.1831076 at 140iterations 6.1134277E-03 0.1079655 at 150iterations 3.6442669E-03 6.2374115E-02 at 160iterations 2.2058017E-03 4.2661667E-02 at 170iterations 1.3707288E-03 2.8484344E-02 at 180iterations finished qdiffx linear iterations at : 04:18:25 total time elapsed so far: 11.10000 # loops : 180 mean,max change (kT/e) : 1.3707288E-03 2.8484344E-02 energy calculations done at 11.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.28000 DelPhi exited at 04:18:26 11.285u 0.163s 0:12.01 95.2% 0+0k 0+0io 0pf+0w