Tue Oct 11 06:09:21 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 06:09:21 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 = 1994 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7502951 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): 3.592000 46.41200 ymin,ymax (A): 0.6220001 40.20600 zmin,zma (A): -2.212000 45.23600 x,y,z range (A): 42.82000 39.58400 47.44800 scale (grids/A): 0.7502951 object centre (A): 25.00200 20.41400 21.51200 number of atom coordinates read : 1994 total number of charged atoms : 1866 net assigned charge : 6.500005 assigned positive charge : 300.3701 centred at (gu) : 90.31344 90.55092 90.61968 assigned negative charge : -293.8702 centred at (gu) : 90.50256 90.50987 90.70185 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7810 nv = 96 ne = 84 npr = 39879 no. pairs analyzed = 39879 no. exposed pairs = 2421 no. arc points = 16745 no. surface atoms = 834 nbur = 1160 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 592 mr = 4553 m= 2 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3703 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1338 ## 119 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8087 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1230844E-07 5.4106959E-08 midg,1,midg; midg,igrid,midg 8.8126676E-08 2.1109092E-07 1,midg,midg; igrid,midg,midg 3.3711990E-07 -8.2014040E-08 gauss-seidel spectral radius is 0.9907260 estimated iterations to convergence 84 setup time was (sec) 0.3600000 now iterating at: 06:09:22 rms-change max change #iterations 0.2522240 34.92357 at 10iterations 3.5349708E-02 4.674561 at 20iterations 5.0249286E-03 0.6801081 at 30iterations 7.8694691E-04 0.1110687 at 40iterations 1.6277895E-04 2.2529602E-02 at 50iterations finished qdiffx linear iterations at : 06:09:24 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.6277895E-04 2.2529602E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 06:09:25 3.323u 0.166s 0:03.90 89.2% 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 06:09:25 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 = 1994 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.250885 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): 3.592000 46.41200 ymin,ymax (A): 0.6220001 40.20600 zmin,zma (A): -2.212000 45.23600 x,y,z range (A): 42.82000 39.58400 47.44800 scale (grids/A): 2.250885 object centre (A): 25.00200 20.41400 21.51200 number of atom coordinates read : 1994 total number of charged atoms : 1866 net assigned charge : 6.500005 assigned positive charge : 300.3701 centred at (gu) : 90.94026 91.65286 91.85921 assigned negative charge : -293.8702 centred at (gu) : 91.50794 91.52991 92.10577 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 82040 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16745 grid for indexing accessible points = 1.400000 m= 34685 mr = 58607 m= 7621 mr = 26765 m= 822 mr = 5291 m= 22 mr = 456 m= 0 mr = 6 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 34065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 48 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 14867 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) : 0.7502951 object centre at (A) : 25.00200 20.41400 21.51200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1412664E-02 2.5748746E-02 midg,1,midg; midg,igrid,midg 6.3069938E-03 4.5205336E-02 1,midg,midg; igrid,midg,midg 6.0439270E-02 1.2125650E-02 gauss-seidel spectral radius is 0.9989368 estimated iterations to convergence 243 setup time was (sec) 0.6300000 now iterating at: 06:09:26 rms-change max change #iterations 4.980197 204.5352 at 10iterations 2.559036 82.09357 at 20iterations 1.315094 40.76172 at 30iterations 0.6770562 20.45782 at 40iterations 0.3490728 11.78543 at 50iterations 0.1786307 4.992355 at 60iterations 9.2038371E-02 2.630684 at 70iterations 4.7241095E-02 1.332239 at 80iterations 2.4351949E-02 0.6625453 at 90iterations 1.2618992E-02 0.3833656 at 100iterations 6.5671904E-03 0.1781502 at 110iterations 3.4258228E-03 0.1046600 at 120iterations finished qdiffx linear iterations at : 06:09:33 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 3.4258228E-03 0.1046600 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 06:09:33 7.762u 0.198s 0:08.25 96.3% 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 06:09:33 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 = 1994 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.376328 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): 3.592000 46.41200 ymin,ymax (A): 0.6220001 40.20600 zmin,zma (A): -2.212000 45.23600 x,y,z range (A): 42.82000 39.58400 47.44800 scale (grids/A): 3.376328 object centre (A): 25.00200 20.41400 21.51200 number of atom coordinates read : 1994 total number of charged atoms : 1866 net assigned charge : 6.500005 assigned positive charge : 300.3701 centred at (gu) : 91.41041 92.47947 92.78871 assigned negative charge : -293.8702 centred at (gu) : 92.26199 92.29485 93.15871 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 188755 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16745 grid for indexing accessible points = 1.400000 m= 106039 mr = 140552 m= 46280 mr = 89018 m= 14615 mr = 38661 m= 3289 mr = 11617 m= 447 mr = 2498 m= 20 mr = 320 m= 0 mr = 5 time to grow re-entrant surface = 0.6800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.280000 number of dielectric boundary points 76774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 14928 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) : 2.250885 object centre at (A) : 25.00200 20.41400 21.51200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4115888 0.3321219 midg,1,midg; midg,igrid,midg -1.3914567E-02 0.3178402 1,midg,midg; igrid,midg,midg 0.4043226 0.2258785 gauss-seidel spectral radius is 0.9993212 estimated iterations to convergence 303 setup time was (sec) 1.510000 now iterating at: 06:09:35 rms-change max change #iterations 10.75188 290.6786 at 10iterations 6.417844 129.2578 at 20iterations 3.834806 73.53984 at 30iterations 2.281260 45.24431 at 40iterations 1.355378 23.40778 at 50iterations 0.8033004 15.58941 at 60iterations 0.4761537 7.877663 at 70iterations 0.2826025 5.037798 at 80iterations 0.1671314 2.586085 at 90iterations 9.8816805E-02 1.704101 at 100iterations 5.8560263E-02 1.000250 at 110iterations 3.4822788E-02 0.5819105 at 120iterations 2.0807315E-02 0.3402519 at 130iterations 1.2579065E-02 0.2061415 at 140iterations 7.7692131E-03 0.1347883 at 150iterations 4.9712816E-03 7.8231812E-02 at 160iterations 3.3324361E-03 5.8715820E-02 at 170iterations 2.3808011E-03 4.2427063E-02 at 180iterations finished qdiffx linear iterations at : 06:09:46 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 2.3808011E-03 4.2427063E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 06:09:47 12.923u 0.210s 0:13.50 97.2% 0+0k 0+0io 0pf+0w