Tue Oct 11 07:01:21 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+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 07:01:21 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2821 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 0.5629259 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): -59.89900 3.342000 ymin,ymax (A): -12.68400 42.36100 zmin,zma (A): 5.399000 54.93500 x,y,z range (A): 63.24100 55.04500 49.53600 scale (grids/A): 0.5629259 object centre (A): -28.27850 14.83850 30.16700 number of atom coordinates read : 2821 total number of charged atoms : 2678 net assigned charge : -3.099990 assigned positive charge : 408.9928 centred at (gu) : 87.59641 89.28052 90.55281 assigned negative charge : -412.0933 centred at (gu) : 87.74279 89.45901 90.55603 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5874 nv = 96 ne = 84 npr = 58209 no. pairs analyzed = 58209 no. exposed pairs = 3468 no. arc points = 24415 no. surface atoms = 1181 nbur = 1640 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 229 mr = 3161 m= 0 mr = 7 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2441 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7544 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3904332E-10 -5.2248667E-10 midg,1,midg; midg,igrid,midg 1.8580217E-09 -2.0884712E-09 1,midg,midg; igrid,midg,midg 2.2074083E-09 -1.1853558E-09 gauss-seidel spectral radius is 0.9837098 estimated iterations to convergence 64 setup time was (sec) 0.5800000 now iterating at: 07:01:22 rms-change max change #iterations 8.2407780E-02 13.09976 at 10iterations 6.0589816E-03 0.9872675 at 20iterations 4.3631942E-04 7.0973217E-02 at 30iterations 3.1661348E-05 5.4321289E-03 at 40iterations 2.2862355E-06 3.8146973E-04 at 50iterations finished qdiffx linear iterations at : 07:01:24 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.2862355E-06 3.8146973E-04 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 07:01:25 3.445u 0.162s 0:04.21 85.5% 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 07:01:25 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2821 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 1.688778 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): -59.89900 3.342000 ymin,ymax (A): -12.68400 42.36100 zmin,zma (A): 5.399000 54.93500 x,y,z range (A): 63.24100 55.04500 49.53600 scale (grids/A): 1.688778 object centre (A): -28.27850 14.83850 30.16700 number of atom coordinates read : 2821 total number of charged atoms : 2678 net assigned charge : -3.099990 assigned positive charge : 408.9928 centred at (gu) : 82.78847 87.84084 91.65771 assigned negative charge : -412.0933 centred at (gu) : 83.22814 88.37676 91.66798 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 64858 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24415 grid for indexing accessible points = 1.400000 m= 21150 mr = 44435 m= 2369 mr = 15319 m= 76 mr = 1245 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1410 time to turn everything in is 0.4900000 number of dielectric boundary points 27444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 199 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 20682 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) : 0.5629259 object centre at (A) : -28.27850 14.83850 30.16700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5036577E-03 8.5514905E-03 midg,1,midg; midg,igrid,midg 8.9905607E-03 -2.0879231E-02 1,midg,midg; igrid,midg,midg -6.1915806E-03 -2.2118939E-02 gauss-seidel spectral radius is 0.9982888 estimated iterations to convergence 192 setup time was (sec) 0.7900000 now iterating at: 07:01:26 rms-change max change #iterations 3.412117 175.5725 at 10iterations 1.450401 53.41163 at 20iterations 0.6220492 22.34990 at 30iterations 0.2647355 9.664019 at 40iterations 0.1134513 3.670403 at 50iterations 4.8496529E-02 1.801922 at 60iterations 2.0818783E-02 0.7476730 at 70iterations 8.8946754E-03 0.3685093 at 80iterations 3.8090164E-03 0.1268253 at 90iterations 1.6361487E-03 5.3564072E-02 at 100iterations 6.9621723E-04 2.3233414E-02 at 110iterations 2.9930091E-04 1.0539055E-02 at 120iterations finished qdiffx linear iterations at : 07:01:33 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 2.9930091E-04 1.0539055E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 07:01:34 7.678u 0.196s 0:08.33 94.3% 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 07:01:34 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2821 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 2.533167 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): -59.89900 3.342000 ymin,ymax (A): -12.68400 42.36100 zmin,zma (A): 5.399000 54.93500 x,y,z range (A): 63.24100 55.04500 49.53600 scale (grids/A): 2.533167 object centre (A): -28.27850 14.83850 30.16700 number of atom coordinates read : 2821 total number of charged atoms : 2678 net assigned charge : -3.099990 assigned positive charge : 408.9928 centred at (gu) : 79.18261 86.76112 92.48644 assigned negative charge : -412.0933 centred at (gu) : 79.84217 87.56495 92.50182 start vw surface at 0.1700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 150296 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24415 grid for indexing accessible points = 1.400000 m= 71965 mr = 108130 m= 22289 mr = 58351 m= 3779 mr = 17599 m= 316 mr = 2577 m= 6 mr = 141 m= 0 mr = 1 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 4741 time to turn everything in is 1.180000 number of dielectric boundary points 61852 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 21408 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) : 1.688778 object centre at (A) : -28.27850 14.83850 30.16700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5426586E-02 0.1461382 midg,1,midg; midg,igrid,midg 0.1728690 -0.3614776 1,midg,midg; igrid,midg,midg -0.1757036 -0.4980647 gauss-seidel spectral radius is 0.9991615 estimated iterations to convergence 273 setup time was (sec) 1.490000 now iterating at: 07:01:35 rms-change max change #iterations 8.602826 386.3200 at 10iterations 4.833874 120.4575 at 20iterations 2.699348 59.27686 at 30iterations 1.506551 31.04321 at 40iterations 0.8366058 18.62020 at 50iterations 0.4656232 9.877129 at 60iterations 0.2580185 5.608337 at 70iterations 0.1430627 3.131676 at 80iterations 7.9239190E-02 1.709846 at 90iterations 4.3876257E-02 0.8713975 at 100iterations 2.4338255E-02 0.5141506 at 110iterations 1.3462288E-02 0.2622173 at 120iterations 7.4381470E-03 0.1631851 at 130iterations 4.1237390E-03 8.3000183E-02 at 140iterations 2.2839904E-03 4.2776108E-02 at 150iterations 1.2647290E-03 2.6765823E-02 at 160iterations 6.9848751E-04 1.4662743E-02 at 170iterations 3.8693059E-04 7.5340271E-03 at 180iterations finished qdiffx linear iterations at : 07:01:46 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 3.8693059E-04 7.5340271E-03 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 07:01:47 12.466u 0.237s 0:13.41 94.6% 0+0k 0+0io 0pf+0w