Sun Oct 9 13:46:43 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 Sun Oct 9 2011 at 13:46:44 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 = 2365 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7030849 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): -5.673000 44.39400 ymin,ymax (A): -14.31200 36.32200 zmin,zma (A): 1.944000 45.21600 x,y,z range (A): 50.06700 50.63400 43.27200 scale (grids/A): 0.7030849 object centre (A): 19.36050 11.00500 23.58000 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500012 assigned positive charge : 361.7971 centred at (gu) : 89.18481 91.30483 90.67037 assigned negative charge : -357.2976 centred at (gu) : 89.18512 91.42693 90.71604 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8108 nv = 96 ne = 84 npr = 46810 no. pairs analyzed = 46810 no. exposed pairs = 3019 no. arc points = 21080 no. surface atoms = 1017 nbur = 1348 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 516 mr = 4481 m= 1 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.1900000 number of dielectric boundary points 4042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2027 ## 194 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8942 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1445621E-08 1.3182308E-08 midg,1,midg; midg,igrid,midg 7.5235100E-08 -3.7190414E-08 1,midg,midg; igrid,midg,midg 4.1381632E-08 3.0123068E-08 gauss-seidel spectral radius is 0.9894904 estimated iterations to convergence 79 setup time was (sec) 0.3800000 now iterating at: 13:46:44 rms-change max change #iterations 0.2088048 28.28992 at 10iterations 2.6054146E-02 3.532593 at 20iterations 3.7767559E-03 0.5546951 at 30iterations 8.4239559E-04 0.1314888 at 40iterations 2.6840612E-04 4.4181824E-02 at 50iterations finished qdiffx linear iterations at : 13:46:47 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.6840612E-04 4.4181824E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 13:46:47 3.402u 0.173s 0:03.86 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 Sun Oct 9 2011 at 13:46:47 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 = 2365 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: 2.109255 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): -5.673000 44.39400 ymin,ymax (A): -14.31200 36.32200 zmin,zma (A): 1.944000 45.21600 x,y,z range (A): 50.06700 50.63400 43.27200 scale (grids/A): 2.109255 object centre (A): 19.36050 11.00500 23.58000 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500012 assigned positive charge : 361.7971 centred at (gu) : 87.55425 93.91402 92.01059 assigned negative charge : -357.2976 centred at (gu) : 87.55497 94.28072 92.14803 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85312 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21080 grid for indexing accessible points = 1.400000 m= 33880 mr = 59264 m= 6506 mr = 25651 m= 643 mr = 4214 m= 19 mr = 378 m= 0 mr = 6 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 284 time to turn everything in is 0.4300000 number of dielectric boundary points 36847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 17683 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) : 0.7030849 object centre at (A) : 19.36050 11.00500 23.58000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3176381E-02 1.2936510E-02 midg,1,midg; midg,igrid,midg 1.2489809E-02 -3.1097425E-02 1,midg,midg; igrid,midg,midg 5.9660573E-02 -1.2204303E-02 gauss-seidel spectral radius is 0.9988570 estimated iterations to convergence 234 setup time was (sec) 0.6600000 now iterating at: 13:46:48 rms-change max change #iterations 4.986783 211.3798 at 10iterations 2.474057 81.68289 at 20iterations 1.234987 37.38007 at 30iterations 0.6157897 17.27733 at 40iterations 0.3080049 9.545197 at 50iterations 0.1547216 4.494956 at 60iterations 7.7503256E-02 2.356140 at 70iterations 3.8755633E-02 1.153013 at 80iterations 1.9620102E-02 0.5530548 at 90iterations 1.0019594E-02 0.2838097 at 100iterations 5.1994752E-03 0.1617126 at 110iterations 2.8086365E-03 8.6132050E-02 at 120iterations finished qdiffx linear iterations at : 13:46:55 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 2.8086365E-03 8.6132050E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 13:46:56 7.959u 0.188s 0:08.40 96.7% 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 Sun Oct 9 2011 at 13:46:56 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 = 2365 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.163882 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): -5.673000 44.39400 ymin,ymax (A): -14.31200 36.32200 zmin,zma (A): 1.944000 45.21600 x,y,z range (A): 50.06700 50.63400 43.27200 scale (grids/A): 3.163882 object centre (A): 19.36050 11.00500 23.58000 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500012 assigned positive charge : 361.7971 centred at (gu) : 86.33112 95.87090 93.01575 assigned negative charge : -357.2976 centred at (gu) : 86.33252 96.42097 93.22189 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 196326 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21080 grid for indexing accessible points = 1.400000 m= 105302 mr = 142789 m= 42918 mr = 86939 m= 12164 mr = 35402 m= 2524 mr = 9293 m= 397 mr = 1905 m= 11 mr = 272 m= 0 mr = 6 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 1014 time to turn everything in is 1.310000 number of dielectric boundary points 83036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 17800 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) : 2.109255 object centre at (A) : 19.36050 11.00500 23.58000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4916034 -9.3536964E-03 midg,1,midg; midg,igrid,midg 0.2819064 -0.3319235 1,midg,midg; igrid,midg,midg 0.6382848 -0.4550668 gauss-seidel spectral radius is 0.9993075 estimated iterations to convergence 300 setup time was (sec) 1.540000 now iterating at: 13:46:58 rms-change max change #iterations 11.10683 468.1242 at 10iterations 6.621262 141.4460 at 20iterations 3.923253 86.32878 at 30iterations 2.324447 43.95939 at 40iterations 1.374717 24.68610 at 50iterations 0.8119827 14.18447 at 60iterations 0.4782674 8.998962 at 70iterations 0.2816410 4.467331 at 80iterations 0.1658244 2.674835 at 90iterations 9.7792894E-02 1.721525 at 100iterations 5.7575651E-02 0.9410057 at 110iterations 3.4038741E-02 0.6569519 at 120iterations 2.0440124E-02 0.3786840 at 130iterations 1.2408320E-02 0.2089071 at 140iterations 7.7985101E-03 0.1538162 at 150iterations 5.1345509E-03 0.1033707 at 160iterations 3.6038237E-03 7.4081421E-02 at 170iterations 2.6952913E-03 5.6087494E-02 at 180iterations finished qdiffx linear iterations at : 13:47:09 total time elapsed so far: 13.07000 # loops : 180 mean,max change (kT/e) : 2.6952913E-03 5.6087494E-02 energy calculations done at 13.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.21000 DelPhi exited at 13:47:10 13.210u 0.211s 0:13.68 98.0% 0+0k 0+0io 0pf+0w