Sat Oct 15 12:52:28 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 15 2011 at 12:52:28 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2625 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 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: 0.6030321 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): 27.20700 81.35400 ymin,ymax (A): -44.98600 14.04900 zmin,zma (A): -15.92200 35.61500 x,y,z range (A): 54.14700 59.03500 51.53700 scale (grids/A): 0.6030321 object centre (A): 54.28050 -15.46850 9.846500 number of atom coordinates read : 2625 total number of charged atoms : 2506 net assigned charge : 2.082025 assigned positive charge : 387.1688 centred at (gu) : 88.89975 90.21886 89.56452 assigned negative charge : -385.0878 centred at (gu) : 88.88837 90.14893 89.61371 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6583 nv = 96 ne = 84 npr = 51095 no. pairs analyzed = 51095 no. exposed pairs = 3651 no. arc points = 26167 no. surface atoms = 1209 nbur = 1416 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 367 mr = 3308 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3300000 number of dielectric boundary points 3616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2621 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8094 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2185898E-09 -8.9234481E-10 midg,1,midg; midg,igrid,midg -1.7342403E-09 3.9184980E-09 1,midg,midg; igrid,midg,midg 6.5530265E-10 1.1176875E-09 gauss-seidel spectral radius is 0.9857836 estimated iterations to convergence 69 setup time was (sec) 0.6700000 now iterating at: 12:52:30 rms-change max change #iterations 0.1058267 15.25198 at 10iterations 9.2171654E-03 1.443702 at 20iterations 7.8234059E-04 0.1185648 at 30iterations 6.7699424E-05 9.8648071E-03 at 40iterations 5.8821211E-06 8.5401535E-04 at 50iterations finished qdiffx linear iterations at : 12:52:39 total time elapsed so far: 5.220000 # loops : 50 mean,max change (kT/e) : 5.8821211E-06 8.5401535E-04 energy calculations done at 5.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.390000 DelPhi exited at 12:52:40 5.391u 0.486s 0:12.61 46.5% 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 Sat Oct 15 2011 at 12:52:40 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2625 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 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: 1.809096 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): 27.20700 81.35400 ymin,ymax (A): -44.98600 14.04900 zmin,zma (A): -15.92200 35.61500 x,y,z range (A): 54.14700 59.03500 51.53700 scale (grids/A): 1.809096 object centre (A): 54.28050 -15.46850 9.846500 number of atom coordinates read : 2625 total number of charged atoms : 2506 net assigned charge : 2.082025 assigned positive charge : 387.1688 centred at (gu) : 86.69871 90.65635 88.69275 assigned negative charge : -385.0878 centred at (gu) : 86.66495 90.44686 88.84111 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70563 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26167 grid for indexing accessible points = 1.400000 m= 24779 mr = 46319 m= 3829 mr = 17408 m= 196 mr = 2184 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 143 time to turn everything in is 0.6300000 number of dielectric boundary points 33409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 197 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19582 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) : 0.6030321 object centre at (A) : 54.28050 -15.46850 9.846500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7615058E-02 1.0003686E-02 midg,1,midg; midg,igrid,midg 7.0564155E-03 8.9557085E-04 1,midg,midg; igrid,midg,midg -7.2130137E-03 -6.4781695E-03 gauss-seidel spectral radius is 0.9985164 estimated iterations to convergence 206 setup time was (sec) 0.9800000 now iterating at: 12:52:42 rms-change max change #iterations 3.785493 174.3961 at 10iterations 1.697663 60.44551 at 20iterations 0.7664368 26.33072 at 30iterations 0.3469210 12.96855 at 40iterations 0.1573529 6.272999 at 50iterations 7.1194537E-02 2.729257 at 60iterations 3.2158054E-02 1.014452 at 70iterations 1.4503867E-02 0.5078897 at 80iterations 6.6140182E-03 0.2085438 at 90iterations 2.9924805E-03 9.9353790E-02 at 100iterations 1.3544594E-03 4.6533585E-02 at 110iterations 6.1448826E-04 2.0019531E-02 at 120iterations finished qdiffx linear iterations at : 12:53:08 total time elapsed so far: 13.60000 # loops : 120 mean,max change (kT/e) : 6.1448826E-04 2.0019531E-02 energy calculations done at 13.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.78000 DelPhi exited at 12:53:09 13.784u 0.522s 0:28.55 50.0% 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 15 2011 at 12:53:09 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2625 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 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: 2.713645 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): 27.20700 81.35400 ymin,ymax (A): -44.98600 14.04900 zmin,zma (A): -15.92200 35.61500 x,y,z range (A): 54.14700 59.03500 51.53700 scale (grids/A): 2.713645 object centre (A): 54.28050 -15.46850 9.846500 number of atom coordinates read : 2625 total number of charged atoms : 2506 net assigned charge : 2.082025 assigned positive charge : 387.1688 centred at (gu) : 85.04799 90.98420 88.03896 assigned negative charge : -385.0878 centred at (gu) : 84.99739 90.67033 88.26179 start vw surface at 0.1300000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 162822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26167 grid for indexing accessible points = 1.400000 m= 79348 mr = 112938 m= 29009 mr = 62756 m= 6795 mr = 22516 m= 769 mr = 4775 m= 43 mr = 433 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 476 time to turn everything in is 1.590000 number of dielectric boundary points 75346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 20040 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) : 1.809096 object centre at (A) : 54.28050 -15.46850 9.846500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1392740 0.1176804 midg,1,midg; midg,igrid,midg 0.2679196 -1.7592188E-02 1,midg,midg; igrid,midg,midg -0.1584746 -0.1336288 gauss-seidel spectral radius is 0.9992364 estimated iterations to convergence 286 setup time was (sec) 2.040000 now iterating at: 12:53:12 rms-change max change #iterations 9.278480 353.2367 at 10iterations 5.385087 125.7524 at 20iterations 3.103175 73.73125 at 30iterations 1.784631 38.74784 at 40iterations 1.022344 20.88384 at 50iterations 0.5840886 11.47036 at 60iterations 0.3336430 6.399078 at 70iterations 0.1902006 4.003977 at 80iterations 0.1083250 2.097429 at 90iterations 6.1604392E-02 1.237804 at 100iterations 3.5122577E-02 0.6941872 at 110iterations 1.9987291E-02 0.3941875 at 120iterations 1.1376069E-02 0.2275314 at 130iterations 6.4776186E-03 0.1221733 at 140iterations 3.6755267E-03 6.5411568E-02 at 150iterations 2.0930048E-03 3.9349556E-02 at 160iterations 1.1902530E-03 2.3679882E-02 at 170iterations 6.7690510E-04 1.2707710E-02 at 180iterations finished qdiffx linear iterations at : 12:53:39 total time elapsed so far: 22.85000 # loops : 180 mean,max change (kT/e) : 6.7690510E-04 1.2707710E-02 energy calculations done at 22.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.02000 DelPhi exited at 12:53:39 23.020u 0.565s 0:30.59 77.0% 0+0k 0+0io 0pf+0w