Tue Oct 11 05:23:06 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 Tue Oct 11 2011 at 05:23:06 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2247 !!! WARNING: MG8 870 has a net charge of 1.4000 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: 0.6905113 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): 19.77200 63.06600 ymin,ymax (A): -3.545000 33.56300 zmin,zma (A): 20.29000 71.84600 x,y,z range (A): 43.29400 37.10800 51.55600 scale (grids/A): 0.6905113 object centre (A): 41.41900 15.00900 46.06800 number of atom coordinates read : 2247 total number of charged atoms : 1938 net assigned charge : 8.900008 assigned positive charge : 314.2170 centred at (gu) : 90.20068 89.65528 89.26832 assigned negative charge : -305.3172 centred at (gu) : 90.36186 89.67297 89.25228 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6762 nv = 96 ne = 84 npr = 41073 no. pairs analyzed = 41073 no. exposed pairs = 2498 no. arc points = 16953 no. surface atoms = 845 nbur = 1402 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3889 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1670 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7553 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1478700E-08 4.8014751E-08 midg,1,midg; midg,igrid,midg 5.9677433E-08 4.1391271E-08 1,midg,midg; igrid,midg,midg 9.8136979E-08 -4.1043222E-09 gauss-seidel spectral radius is 0.9890703 estimated iterations to convergence 78 setup time was (sec) 0.5000000 now iterating at: 05:23:07 rms-change max change #iterations 0.1786487 26.92728 at 10iterations 2.1017719E-02 3.701380 at 20iterations 2.4386444E-03 0.3240242 at 30iterations 2.8889082E-04 3.8864136E-02 at 40iterations 3.3997509E-05 4.8866272E-03 at 50iterations finished qdiffx linear iterations at : 05:23:09 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 3.3997509E-05 4.8866272E-03 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 05:23:10 3.250u 0.181s 0:03.95 86.8% 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 05:23:10 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2247 !!! WARNING: MG8 870 has a net charge of 1.4000 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: 2.071534 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): 19.77200 63.06600 ymin,ymax (A): -3.545000 33.56300 zmin,zma (A): 20.29000 71.84600 x,y,z range (A): 43.29400 37.10800 51.55600 scale (grids/A): 2.071534 object centre (A): 41.41900 15.00900 46.06800 number of atom coordinates read : 2247 total number of charged atoms : 1938 net assigned charge : 8.900008 assigned positive charge : 314.2170 centred at (gu) : 90.60236 88.96578 87.80481 assigned negative charge : -305.3172 centred at (gu) : 91.08562 89.01894 87.75683 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 71301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16953 grid for indexing accessible points = 1.400000 m= 28659 mr = 50796 m= 5479 mr = 21892 m= 474 mr = 3659 m= 11 mr = 262 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 29315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 15362 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) : 0.6905113 object centre at (A) : 41.41900 15.00900 46.06800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8851305E-02 4.6448119E-02 midg,1,midg; midg,igrid,midg 2.5463220E-02 1.4701559E-02 1,midg,midg; igrid,midg,midg 4.1190676E-02 1.8832644E-02 gauss-seidel spectral radius is 0.9987778 estimated iterations to convergence 226 setup time was (sec) 0.8500000 now iterating at: 05:23:11 rms-change max change #iterations 4.354916 215.3514 at 10iterations 2.128145 81.27063 at 20iterations 1.030397 36.50051 at 30iterations 0.5066913 17.44103 at 40iterations 0.2467937 7.909695 at 50iterations 0.1202355 3.917349 at 60iterations 5.8536746E-02 1.957647 at 70iterations 2.8665874E-02 0.9145660 at 80iterations 1.3990299E-02 0.4579735 at 90iterations 6.8516987E-03 0.1938765 at 100iterations 3.3507308E-03 0.1026220 at 110iterations 1.6412160E-03 5.0175190E-02 at 120iterations finished qdiffx linear iterations at : 05:23:18 total time elapsed so far: 7.180000 # loops : 120 mean,max change (kT/e) : 1.6412160E-03 5.0175190E-02 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.360000 DelPhi exited at 05:23:18 7.358u 0.211s 0:08.11 93.2% 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 05:23:18 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2247 !!! WARNING: MG8 870 has a net charge of 1.4000 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: 3.107301 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): 19.77200 63.06600 ymin,ymax (A): -3.545000 33.56300 zmin,zma (A): 20.29000 71.84600 x,y,z range (A): 43.29400 37.10800 51.55600 scale (grids/A): 3.107301 object centre (A): 41.41900 15.00900 46.06800 number of atom coordinates read : 2247 total number of charged atoms : 1938 net assigned charge : 8.900008 assigned positive charge : 314.2170 centred at (gu) : 90.90352 88.44865 86.70718 assigned negative charge : -305.3172 centred at (gu) : 91.62849 88.52836 86.63529 start vw surface at 0.1500000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 164431 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16953 grid for indexing accessible points = 1.400000 m= 89623 mr = 122395 m= 36158 mr = 74745 m= 10125 mr = 29780 m= 1900 mr = 7909 m= 205 mr = 1400 m= 2 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.620000 number of dielectric boundary points 66071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 15504 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) : 2.071534 object centre at (A) : 41.41900 15.00900 46.06800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4634057 0.3320451 midg,1,midg; midg,igrid,midg 0.2254538 0.1246929 1,midg,midg; igrid,midg,midg 0.3398991 0.3237268 gauss-seidel spectral radius is 0.9992805 estimated iterations to convergence 294 setup time was (sec) 1.910000 now iterating at: 05:23:20 rms-change max change #iterations 9.854902 436.9451 at 10iterations 5.814161 165.0961 at 20iterations 3.417992 69.26532 at 30iterations 2.001866 40.95063 at 40iterations 1.170751 28.24171 at 50iterations 0.6842846 16.54885 at 60iterations 0.3988185 8.394519 at 70iterations 0.2332736 4.283107 at 80iterations 0.1359937 2.349371 at 90iterations 7.9074666E-02 1.451928 at 100iterations 4.6093501E-02 0.8514824 at 110iterations 2.6864870E-02 0.5733986 at 120iterations 1.5610469E-02 0.2749290 at 130iterations 9.1336844E-03 0.1747360 at 140iterations 5.3624581E-03 0.1083579 at 150iterations 3.1674043E-03 5.5446625E-02 at 160iterations 1.8971945E-03 3.6293030E-02 at 170iterations 1.1637182E-03 2.3591995E-02 at 180iterations finished qdiffx linear iterations at : 05:23:31 total time elapsed so far: 12.03000 # loops : 180 mean,max change (kT/e) : 1.1637182E-03 2.3591995E-02 energy calculations done at 12.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 05:23:31 12.205u 0.234s 0:12.93 96.1% 0+0k 0+0io 0pf+0w