Sat Oct 8 19:39:20 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 Sat Oct 8 2011 at 19:39:20 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 = 2565 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6193781 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): -10.31800 38.77700 ymin,ymax (A): -22.47300 24.94900 zmin,zma (A): -12.43100 45.04600 x,y,z range (A): 49.09500 47.42200 57.47700 scale (grids/A): 0.6193781 object centre (A): 14.22950 1.238000 16.30750 number of atom coordinates read : 2565 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 88.48887 89.31111 89.68237 assigned negative charge : -386.5045 centred at (gu) : 88.38665 89.38320 89.56137 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6415 nv = 96 ne = 84 npr = 52688 no. pairs analyzed = 52688 no. exposed pairs = 2953 no. arc points = 21373 no. surface atoms = 1001 nbur = 1564 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 307 mr = 3556 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 131 time to turn everything in is 0.2700000 number of dielectric boundary points 3129 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2145 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8016 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4660791E-09 9.8883000E-09 midg,1,midg; midg,igrid,midg 8.7422816E-09 -1.5562137E-09 1,midg,midg; igrid,midg,midg -5.4680407E-09 6.7644139E-09 gauss-seidel spectral radius is 0.9864956 estimated iterations to convergence 70 setup time was (sec) 0.5100000 now iterating at: 19:39:21 rms-change max change #iterations 0.1231904 18.55087 at 10iterations 1.1397187E-02 1.737900 at 20iterations 1.0775378E-03 0.1723132 at 30iterations 9.9617588E-05 1.3572693E-02 at 40iterations 9.7046286E-06 1.4936924E-03 at 50iterations finished qdiffx linear iterations at : 19:39:23 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 9.7046286E-06 1.4936924E-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) 3.260000 DelPhi exited at 19:39:24 3.260u 0.177s 0:03.71 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 Sat Oct 8 2011 at 19:39:24 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 = 2565 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: 1.858135 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): -10.31800 38.77700 ymin,ymax (A): -22.47300 24.94900 zmin,zma (A): -12.43100 45.04600 x,y,z range (A): 49.09500 47.42200 57.47700 scale (grids/A): 1.858135 object centre (A): 14.22950 1.238000 16.30750 number of atom coordinates read : 2565 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 85.46639 87.93266 89.04678 assigned negative charge : -386.5045 centred at (gu) : 85.15991 88.14924 88.68422 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21373 grid for indexing accessible points = 1.400000 m= 24228 mr = 49073 m= 3354 mr = 17949 m= 181 mr = 2028 m= 4 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 5031 time to turn everything in is 0.5000000 number of dielectric boundary points 28888 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19224 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) : 0.6193781 object centre at (A) : 14.22950 1.238000 16.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8467553E-02 3.3775322E-02 midg,1,midg; midg,igrid,midg 1.4274962E-02 2.9562637E-03 1,midg,midg; igrid,midg,midg -8.8715600E-03 2.9084703E-02 gauss-seidel spectral radius is 0.9985633 estimated iterations to convergence 209 setup time was (sec) 0.7900000 now iterating at: 19:39:25 rms-change max change #iterations 3.985500 182.1732 at 10iterations 1.826667 71.34155 at 20iterations 0.8412158 29.42579 at 30iterations 0.3851704 13.67351 at 40iterations 0.1776268 6.742595 at 50iterations 8.1374615E-02 2.438034 at 60iterations 3.7423704E-02 1.203406 at 70iterations 1.7138749E-02 0.5327289 at 80iterations 7.8845881E-03 0.2657127 at 90iterations 3.6355788E-03 0.1243534 at 100iterations 1.6705233E-03 5.2587509E-02 at 110iterations 7.6925883E-04 2.7425289E-02 at 120iterations finished qdiffx linear iterations at : 19:39:31 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 7.6925883E-04 2.7425289E-02 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.340000 DelPhi exited at 19:39:32 7.342u 0.208s 0:07.85 96.0% 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 Sat Oct 8 2011 at 19:39:32 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 = 2565 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: 2.787202 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): -10.31800 38.77700 ymin,ymax (A): -22.47300 24.94900 zmin,zma (A): -12.43100 45.04600 x,y,z range (A): 49.09500 47.42200 57.47700 scale (grids/A): 2.787202 object centre (A): 14.22950 1.238000 16.30750 number of atom coordinates read : 2565 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 83.19935 86.89895 88.57010 assigned negative charge : -386.5045 centred at (gu) : 82.73982 87.22372 88.02626 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 162358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21373 grid for indexing accessible points = 1.400000 m= 80443 mr = 118453 m= 27332 mr = 66461 m= 6020 mr = 21878 m= 760 mr = 4470 m= 38 mr = 477 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 17340 time to turn everything in is 1.210000 number of dielectric boundary points 65193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 19623 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) : 1.858135 object centre at (A) : 14.22950 1.238000 16.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6769501E-02 0.5013784 midg,1,midg; midg,igrid,midg 0.1621523 2.0254044E-02 1,midg,midg; igrid,midg,midg -6.7156889E-02 0.4002568 gauss-seidel spectral radius is 0.9992329 estimated iterations to convergence 285 setup time was (sec) 1.510000 now iterating at: 19:39:33 rms-change max change #iterations 9.399221 343.5243 at 10iterations 5.404743 127.6009 at 20iterations 3.089876 65.56917 at 30iterations 1.761226 38.27537 at 40iterations 1.002283 19.51068 at 50iterations 0.5704504 11.44554 at 60iterations 0.3249778 6.628687 at 70iterations 0.1845348 3.537531 at 80iterations 0.1050369 1.995468 at 90iterations 5.9740979E-02 1.159252 at 100iterations 3.3939824E-02 0.6815205 at 110iterations 1.9338278E-02 0.3763123 at 120iterations 1.0995302E-02 0.2020416 at 130iterations 6.2464150E-03 0.1213379 at 140iterations 3.5535374E-03 7.1416855E-02 at 150iterations 2.0225830E-03 3.8166046E-02 at 160iterations 1.1504629E-03 2.1171808E-02 at 170iterations 6.5834873E-04 1.2306213E-02 at 180iterations finished qdiffx linear iterations at : 19:39:45 total time elapsed so far: 13.01000 # loops : 180 mean,max change (kT/e) : 6.5834873E-04 1.2306213E-02 energy calculations done at 13.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.19000 DelPhi exited at 19:39:46 13.187u 0.219s 0:13.70 97.7% 0+0k 0+0io 0pf+0w