Tue Oct 11 06:42:44 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 06:42:45 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 = 2080 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: 0.7179157 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): -36.43400 9.380000 ymin,ymax (A): -3.716000 33.24000 zmin,zma (A): 20.27500 69.86300 x,y,z range (A): 45.81400 36.95600 49.58800 scale (grids/A): 0.7179157 object centre (A): -13.52700 14.76200 45.06900 number of atom coordinates read : 2080 total number of charged atoms : 1952 net assigned charge : 6.500009 assigned positive charge : 316.5260 centred at (gu) : 90.62231 89.54206 88.67257 assigned negative charge : -310.0262 centred at (gu) : 90.75477 89.56811 88.61175 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6860 nv = 96 ne = 84 npr = 43542 no. pairs analyzed = 43542 no. exposed pairs = 2396 no. arc points = 16427 no. surface atoms = 820 nbur = 1260 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 409 mr = 3921 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.1900000 number of dielectric boundary points 3285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1502 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7903 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1801332E-08 8.4378890E-08 midg,1,midg; midg,igrid,midg 9.4841866E-08 5.0489145E-08 1,midg,midg; igrid,midg,midg 1.3468183E-07 -1.3993115E-08 gauss-seidel spectral radius is 0.9898754 estimated iterations to convergence 81 setup time was (sec) 0.3700000 now iterating at: 06:42:46 rms-change max change #iterations 0.2149217 35.44065 at 10iterations 2.7728599E-02 3.608168 at 20iterations 3.4576387E-03 0.4649200 at 30iterations 4.5394205E-04 6.3821793E-02 at 40iterations 5.9538583E-05 7.1096420E-03 at 50iterations finished qdiffx linear iterations at : 06:42:48 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 5.9538583E-05 7.1096420E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 06:42:50 3.381u 0.183s 0:05.57 63.9% 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 06:42:51 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 = 2080 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: 2.153747 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): -36.43400 9.380000 ymin,ymax (A): -3.716000 33.24000 zmin,zma (A): 20.27500 69.86300 x,y,z range (A): 45.81400 36.95600 49.58800 scale (grids/A): 2.153747 object centre (A): -13.52700 14.76200 45.06900 number of atom coordinates read : 2080 total number of charged atoms : 1952 net assigned charge : 6.500009 assigned positive charge : 316.5260 centred at (gu) : 91.86703 88.62630 86.01771 assigned negative charge : -310.0262 centred at (gu) : 92.26450 88.70438 85.83550 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 73528 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16427 grid for indexing accessible points = 1.400000 m= 27202 mr = 52248 m= 4905 mr = 20176 m= 474 mr = 3167 m= 12 mr = 253 m= 0 mr = 6 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1679 time to turn everything in is 0.3900000 number of dielectric boundary points 30271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15529 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) : 0.7179157 object centre at (A) : -13.52700 14.76200 45.06900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2119561E-02 6.4328283E-02 midg,1,midg; midg,igrid,midg 3.0015070E-02 1.1104214E-02 1,midg,midg; igrid,midg,midg 3.3803925E-02 1.8390628E-02 gauss-seidel spectral radius is 0.9988515 estimated iterations to convergence 234 setup time was (sec) 0.6100000 now iterating at: 06:42:52 rms-change max change #iterations 4.697188 172.8171 at 10iterations 2.329356 72.53455 at 20iterations 1.164161 36.44051 at 30iterations 0.5799477 21.25550 at 40iterations 0.2898488 9.611390 at 50iterations 0.1451097 4.120138 at 60iterations 7.2401837E-02 2.061611 at 70iterations 3.6003396E-02 1.205350 at 80iterations 1.8023038E-02 0.5717673 at 90iterations 9.0347612E-03 0.2832527 at 100iterations 4.4895122E-03 0.1323395 at 110iterations 2.2474998E-03 6.6691399E-02 at 120iterations finished qdiffx linear iterations at : 06:42:59 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 2.2474998E-03 6.6691399E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 06:42:59 7.888u 0.208s 0:08.76 92.2% 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 06:43:00 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 = 2080 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: 3.230620 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): -36.43400 9.380000 ymin,ymax (A): -3.716000 33.24000 zmin,zma (A): 20.27500 69.86300 x,y,z range (A): 45.81400 36.95600 49.58800 scale (grids/A): 3.230620 object centre (A): -13.52700 14.76200 45.06900 number of atom coordinates read : 2080 total number of charged atoms : 1952 net assigned charge : 6.500009 assigned positive charge : 316.5260 centred at (gu) : 92.80026 87.93935 84.02644 assigned negative charge : -310.0262 centred at (gu) : 93.39670 88.05670 83.75322 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 170014 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16427 grid for indexing accessible points = 1.400000 m= 87032 mr = 126301 m= 32926 mr = 71558 m= 9100 mr = 26634 m= 1894 mr = 6883 m= 264 mr = 1423 m= 11 mr = 175 m= 0 mr = 7 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 5598 time to turn everything in is 1.120000 number of dielectric boundary points 68260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 15616 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) : 2.153747 object centre at (A) : -13.52700 14.76200 45.06900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3644262 0.4903406 midg,1,midg; midg,igrid,midg 0.2458560 7.6022543E-02 1,midg,midg; igrid,midg,midg 0.2847503 0.4329588 gauss-seidel spectral radius is 0.9992971 estimated iterations to convergence 298 setup time was (sec) 1.350000 now iterating at: 06:43:01 rms-change max change #iterations 10.36414 344.4183 at 10iterations 6.118671 155.8054 at 20iterations 3.607383 78.73782 at 30iterations 2.119964 37.71604 at 40iterations 1.244818 22.06439 at 50iterations 0.7312043 12.96537 at 60iterations 0.4290222 7.809140 at 70iterations 0.2514415 4.634369 at 80iterations 0.1474345 2.680492 at 90iterations 8.6315252E-02 1.637595 at 100iterations 5.0477467E-02 0.7994442 at 110iterations 2.9565422E-02 0.5465984 at 120iterations 1.7378081E-02 0.3144939 at 130iterations 1.0244049E-02 0.1878128 at 140iterations 6.0731415E-03 0.1015654 at 150iterations 3.6429695E-03 6.1473846E-02 at 160iterations 2.2289229E-03 4.5619965E-02 at 170iterations 1.3999550E-03 2.5944710E-02 at 180iterations finished qdiffx linear iterations at : 06:43:12 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 1.3999550E-03 2.5944710E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 06:43:13 12.884u 0.224s 0:13.49 97.1% 0+0k 0+0io 0pf+0w