Tue Oct 11 07:51:59 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 07:51:59 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2381 !!! WARNING: SEP 192 has a net charge of -0.4750 !!! WARNING: GLM 194 has a net charge of -0.0940 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: 0.6362938 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): -8.994000 36.34200 ymin,ymax (A): -14.97400 40.97500 zmin,zma (A): 5.189000 52.42600 x,y,z range (A): 45.33600 55.94900 47.23700 scale (grids/A): 0.6362938 object centre (A): 13.67400 13.00050 28.80750 number of atom coordinates read : 2381 total number of charged atoms : 2239 net assigned charge : 3.931009 assigned positive charge : 356.8413 centred at (gu) : 90.53283 88.80573 90.73587 assigned negative charge : -352.9108 centred at (gu) : 90.45073 88.81445 90.88946 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6487 nv = 96 ne = 84 npr = 48076 no. pairs analyzed = 48076 no. exposed pairs = 2881 no. arc points = 20107 no. surface atoms = 980 nbur = 1401 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 372 mr = 3639 m= 2 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2050 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7753 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6773047E-08 -1.1494889E-08 midg,1,midg; midg,igrid,midg 7.7733899E-09 3.4292031E-09 1,midg,midg; igrid,midg,midg -2.3839000E-09 1.4570081E-08 gauss-seidel spectral radius is 0.9871832 estimated iterations to convergence 72 setup time was (sec) 0.5600000 now iterating at: 07:52:00 rms-change max change #iterations 0.1373845 21.14304 at 10iterations 1.3885931E-02 2.054454 at 20iterations 1.6490649E-03 0.2475758 at 30iterations 2.7706797E-04 4.2770386E-02 at 40iterations 6.0889419E-05 9.0751648E-03 at 50iterations finished qdiffx linear iterations at : 07:52:03 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 6.0889419E-05 9.0751648E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 07:52:03 3.345u 0.192s 0:04.07 86.7% 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 07:52:03 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2381 !!! WARNING: SEP 192 has a net charge of -0.4750 !!! WARNING: GLM 194 has a net charge of -0.0940 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: 1.908881 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): -8.994000 36.34200 ymin,ymax (A): -14.97400 40.97500 zmin,zma (A): 5.189000 52.42600 x,y,z range (A): 45.33600 55.94900 47.23700 scale (grids/A): 1.908881 object centre (A): 13.67400 13.00050 28.80750 number of atom coordinates read : 2381 total number of charged atoms : 2239 net assigned charge : 3.931009 assigned positive charge : 356.8413 centred at (gu) : 91.59809 86.41666 92.20746 assigned negative charge : -352.9108 centred at (gu) : 91.35217 86.44308 92.66822 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69552 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20107 grid for indexing accessible points = 1.400000 m= 26524 mr = 48649 m= 4333 mr = 20021 m= 247 mr = 2766 m= 4 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 29113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 17566 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) : 0.6362938 object centre at (A) : 13.67400 13.00050 28.80750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4508411E-02 -2.4398364E-02 midg,1,midg; midg,igrid,midg 1.7526038E-02 3.2071870E-02 1,midg,midg; igrid,midg,midg -5.3134798E-03 6.0420767E-03 gauss-seidel spectral radius is 0.9986176 estimated iterations to convergence 213 setup time was (sec) 0.7900000 now iterating at: 07:52:04 rms-change max change #iterations 4.022318 167.0822 at 10iterations 1.874718 70.02647 at 20iterations 0.8813220 30.90606 at 30iterations 0.4094793 13.21736 at 40iterations 0.1928301 6.527093 at 50iterations 8.9979753E-02 2.971100 at 60iterations 4.1984551E-02 1.474920 at 70iterations 1.9682333E-02 0.6310444 at 80iterations 9.2393728E-03 0.2979050 at 90iterations 4.3555731E-03 0.1481047 at 100iterations 2.0745525E-03 7.7381134E-02 at 110iterations 1.0031733E-03 3.2217026E-02 at 120iterations finished qdiffx linear iterations at : 07:52:11 total time elapsed so far: 7.210000 # loops : 120 mean,max change (kT/e) : 1.0031733E-03 3.2217026E-02 energy calculations done at 7.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.390000 DelPhi exited at 07:52:11 7.395u 0.221s 0:08.24 92.3% 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 07:52:12 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2381 !!! WARNING: SEP 192 has a net charge of -0.4750 !!! WARNING: GLM 194 has a net charge of -0.0940 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: 2.863322 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): -8.994000 36.34200 ymin,ymax (A): -14.97400 40.97500 zmin,zma (A): 5.189000 52.42600 x,y,z range (A): 45.33600 55.94900 47.23700 scale (grids/A): 2.863322 object centre (A): 13.67400 13.00050 28.80750 number of atom coordinates read : 2381 total number of charged atoms : 2239 net assigned charge : 3.931009 assigned positive charge : 356.8413 centred at (gu) : 92.39700 84.62476 93.31100 assigned negative charge : -352.9108 centred at (gu) : 92.02829 84.66472 94.00230 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 160582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20107 grid for indexing accessible points = 1.400000 m= 84674 mr = 117586 m= 31867 mr = 70018 m= 7755 mr = 25970 m= 1135 mr = 5976 m= 79 mr = 783 m= 0 mr = 46 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.280000 number of dielectric boundary points 65713 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 17906 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) : 1.908881 object centre at (A) : 13.67400 13.00050 28.80750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3787157 -0.3310944 midg,1,midg; midg,igrid,midg 0.1378583 0.3413572 1,midg,midg; igrid,midg,midg -3.6518071E-02 -1.0927006E-02 gauss-seidel spectral radius is 0.9992465 estimated iterations to convergence 288 setup time was (sec) 1.570000 now iterating at: 07:52:13 rms-change max change #iterations 9.500254 295.8904 at 10iterations 5.549594 171.6559 at 20iterations 3.221499 68.29743 at 30iterations 1.860138 40.39435 at 40iterations 1.073558 20.95940 at 50iterations 0.6179231 12.22474 at 60iterations 0.3549572 7.047332 at 70iterations 0.2036640 3.924076 at 80iterations 0.1169899 2.245598 at 90iterations 6.7046218E-02 1.373118 at 100iterations 3.8478304E-02 0.8096466 at 110iterations 2.2020405E-02 0.4184418 at 120iterations 1.2636834E-02 0.2310677 at 130iterations 7.2475048E-03 0.1481590 at 140iterations 4.1730227E-03 8.0707550E-02 at 150iterations 2.4132261E-03 4.6131134E-02 at 160iterations 1.4086590E-03 2.9256821E-02 at 170iterations 8.3630858E-04 1.6296387E-02 at 180iterations finished qdiffx linear iterations at : 07:52:24 total time elapsed so far: 11.78000 # loops : 180 mean,max change (kT/e) : 8.3630858E-04 1.6296387E-02 energy calculations done at 11.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 07:52:24 11.971u 0.215s 0:12.89 94.4% 0+0k 0+0io 0pf+0w