Tue Oct 11 08:10:53 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 08:10:53 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1227 !!! WARNING: GLM 66 has a net charge of -0.0940 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: ZN2 203 has a net charge of 1.4000 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: 0.7422853 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): 12.79100 51.66000 ymin,ymax (A): -32.46000 11.70400 zmin,zma (A): -23.66100 24.29900 x,y,z range (A): 38.86900 44.16400 47.96000 scale (grids/A): 0.7422853 object centre (A): 32.22550 -10.37800 0.3190002 number of atom coordinates read : 1227 total number of charged atoms : 1135 net assigned charge : 0.5060054 assigned positive charge : 183.6561 centred at (gu) : 90.13579 87.90989 92.00741 assigned negative charge : -183.1502 centred at (gu) : 89.99361 87.99583 91.85313 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4782 nv = 96 ne = 84 npr = 23345 no. pairs analyzed = 23345 no. exposed pairs = 1846 no. arc points = 13505 no. surface atoms = 616 nbur = 611 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 322 mr = 2186 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 2889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1059 ## 73 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 4831 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.0469624E-08 1.4412751E-07 midg,1,midg; midg,igrid,midg 8.5952962E-08 -3.1076471E-08 1,midg,midg; igrid,midg,midg -7.9011244E-08 9.3174549E-08 gauss-seidel spectral radius is 0.9904596 estimated iterations to convergence 83 setup time was (sec) 0.4100000 now iterating at: 08:10:53 rms-change max change #iterations 0.1915917 35.10675 at 10iterations 2.5138993E-02 4.205578 at 20iterations 3.3371144E-03 0.5949278 at 30iterations 4.4153034E-04 7.7384949E-02 at 40iterations 5.7928002E-05 9.7417831E-03 at 50iterations finished qdiffx linear iterations at : 08:10:56 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 5.7928002E-05 9.7417831E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 08:10:57 3.380u 0.163s 0:04.05 87.4% 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 Tue Oct 11 2011 at 08:10:57 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1227 !!! WARNING: GLM 66 has a net charge of -0.0940 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: ZN2 203 has a net charge of 1.4000 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: 2.226856 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): 12.79100 51.66000 ymin,ymax (A): -32.46000 11.70400 zmin,zma (A): -23.66100 24.29900 x,y,z range (A): 38.86900 44.16400 47.96000 scale (grids/A): 2.226856 object centre (A): 32.22550 -10.37800 0.3190002 number of atom coordinates read : 1227 total number of charged atoms : 1135 net assigned charge : 0.5060054 assigned positive charge : 183.6561 centred at (gu) : 90.40739 83.72984 96.02254 assigned negative charge : -183.1502 centred at (gu) : 89.98108 83.98771 95.55968 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 49436 reading accessible surface arcs data from file ARCDAT no. of arc points read = 13505 grid for indexing accessible points = 1.400000 m= 17221 mr = 30348 m= 3417 mr = 11668 m= 293 mr = 1886 m= 13 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 26402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 9039 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) : 0.7422853 object centre at (A) : 32.22550 -10.37800 0.3190002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2481955E-04 1.4621043E-02 midg,1,midg; midg,igrid,midg -1.0979298E-02 -1.3564733E-02 1,midg,midg; igrid,midg,midg 6.2904280E-04 1.7891444E-02 gauss-seidel spectral radius is 0.9988530 estimated iterations to convergence 234 setup time was (sec) 0.7600000 now iterating at: 08:10:58 rms-change max change #iterations 3.814602 220.5839 at 10iterations 1.885123 79.72475 at 20iterations 0.9413327 38.06095 at 30iterations 0.4664602 18.09981 at 40iterations 0.2304943 9.417082 at 50iterations 0.1143832 4.314747 at 60iterations 5.6758806E-02 2.193737 at 70iterations 2.8277291E-02 0.9672775 at 80iterations 1.3929739E-02 0.5012598 at 90iterations 6.9709793E-03 0.2910652 at 100iterations 3.4390828E-03 0.1191106 at 110iterations 1.7051413E-03 6.6009521E-02 at 120iterations finished qdiffx linear iterations at : 08:11:05 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 1.7051413E-03 6.6009521E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 08:11:05 7.615u 0.171s 0:08.32 93.5% 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 08:11:05 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1227 !!! WARNING: GLM 66 has a net charge of -0.0940 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: ZN2 203 has a net charge of 1.4000 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: 3.340284 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): 12.79100 51.66000 ymin,ymax (A): -32.46000 11.70400 zmin,zma (A): -23.66100 24.29900 x,y,z range (A): 38.86900 44.16400 47.96000 scale (grids/A): 3.340284 object centre (A): 32.22550 -10.37800 0.3190002 number of atom coordinates read : 1227 total number of charged atoms : 1135 net assigned charge : 0.5060054 assigned positive charge : 183.6561 centred at (gu) : 90.61113 80.59476 99.03374 assigned negative charge : -183.1502 centred at (gu) : 89.97171 80.98155 98.33968 start vw surface at 0.1100000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 113530 reading accessible surface arcs data from file ARCDAT no. of arc points read = 13505 grid for indexing accessible points = 1.400000 m= 53700 mr = 73908 m= 21020 mr = 41528 m= 6162 mr = 15912 m= 1170 mr = 4261 m= 96 mr = 594 m= 0 mr = 29 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 59446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 9080 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) : 2.226856 object centre at (A) : 32.22550 -10.37800 0.3190002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6681748E-02 0.1368748 midg,1,midg; midg,igrid,midg -8.1366282E-03 -0.1236524 1,midg,midg; igrid,midg,midg 3.0538494E-02 0.1197278 gauss-seidel spectral radius is 0.9993196 estimated iterations to convergence 302 setup time was (sec) 1.590000 now iterating at: 08:11:07 rms-change max change #iterations 8.502791 291.5841 at 10iterations 5.051147 124.2258 at 20iterations 2.986497 65.27526 at 30iterations 1.754015 39.01363 at 40iterations 1.029296 22.52319 at 50iterations 0.6040276 14.43889 at 60iterations 0.3540888 7.523053 at 70iterations 0.2076883 4.307178 at 80iterations 0.1213185 2.480907 at 90iterations 7.0990570E-02 1.541855 at 100iterations 4.1616909E-02 0.8490677 at 110iterations 2.4336396E-02 0.5068189 at 120iterations 1.4262682E-02 0.3159065 at 130iterations 8.3321799E-03 0.1743050 at 140iterations 4.8810979E-03 0.1027431 at 150iterations 2.8608122E-03 6.8031311E-02 at 160iterations 1.6775351E-03 3.3962250E-02 at 170iterations 9.8047755E-04 2.1141052E-02 at 180iterations finished qdiffx linear iterations at : 08:11:19 total time elapsed so far: 13.44000 # loops : 180 mean,max change (kT/e) : 9.8047755E-04 2.1141052E-02 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.63000 DelPhi exited at 08:11:20 13.631u 0.185s 0:14.42 95.7% 0+0k 0+0io 0pf+0w