Tue Oct 11 06:11:19 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 Tue Oct 11 2011 at 06:11:19 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 = 2043 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: 0.7043368 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): 27.06500 70.73000 ymin,ymax (A): 43.91700 82.06900 zmin,zma (A): -60.27600 -9.732000 x,y,z range (A): 43.66500 38.15200 50.54400 scale (grids/A): 0.7043368 object centre (A): 48.89750 62.99300 -35.00400 number of atom coordinates read : 2043 total number of charged atoms : 1913 net assigned charge : 5.500006 assigned positive charge : 307.9621 centred at (gu) : 90.58210 89.47592 89.06818 assigned negative charge : -302.4622 centred at (gu) : 90.73049 89.55864 89.09290 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7024 nv = 96 ne = 84 npr = 40592 no. pairs analyzed = 40592 no. exposed pairs = 2625 no. arc points = 17565 no. surface atoms = 883 nbur = 1160 mkacc time = 7.9999983E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 509 mr = 4014 m= 6 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1590 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7630 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4881320E-08 2.7103264E-08 midg,1,midg; midg,igrid,midg 8.8452246E-08 5.6238783E-09 1,midg,midg; igrid,midg,midg 9.6885735E-08 -2.7380322E-08 gauss-seidel spectral radius is 0.9894919 estimated iterations to convergence 79 setup time was (sec) 0.5400000 now iterating at: 06:11:20 rms-change max change #iterations 0.1944533 27.11198 at 10iterations 2.4617609E-02 3.267173 at 20iterations 3.5609654E-03 0.5175018 at 30iterations 8.4085343E-04 0.1030254 at 40iterations 2.8660620E-04 3.6216736E-02 at 50iterations finished qdiffx linear iterations at : 06:11:22 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 2.8660620E-04 3.6216736E-02 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 06:11:23 3.134u 0.144s 0:03.65 89.5% 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 06:11:23 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 = 2043 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: 2.113010 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): 27.06500 70.73000 ymin,ymax (A): 43.91700 82.06900 zmin,zma (A): -60.27600 -9.732000 x,y,z range (A): 43.66500 38.15200 50.54400 scale (grids/A): 2.113010 object centre (A): 48.89750 62.99300 -35.00400 number of atom coordinates read : 2043 total number of charged atoms : 1913 net assigned charge : 5.500006 assigned positive charge : 307.9621 centred at (gu) : 91.74619 88.42762 87.20451 assigned negative charge : -302.4622 centred at (gu) : 92.19166 88.67598 87.27885 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73803 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17565 grid for indexing accessible points = 1.400000 m= 30820 mr = 52257 m= 6267 mr = 23359 m= 611 mr = 4204 m= 18 mr = 285 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 31414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 15162 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) : 0.7043368 object centre at (A) : 48.89750 62.99300 -35.00400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2408187E-02 1.9741124E-02 midg,1,midg; midg,igrid,midg 3.2909229E-02 -4.9954075E-03 1,midg,midg; igrid,midg,midg 3.6909685E-02 8.9679109E-03 gauss-seidel spectral radius is 0.9988227 estimated iterations to convergence 231 setup time was (sec) 0.9000000 now iterating at: 06:11:24 rms-change max change #iterations 4.487523 181.4945 at 10iterations 2.228264 73.16626 at 20iterations 1.099397 33.87229 at 30iterations 0.5427999 17.37772 at 40iterations 0.2699844 8.478291 at 50iterations 0.1334931 4.064499 at 60iterations 6.6586174E-02 2.141705 at 70iterations 3.3122227E-02 0.9041634 at 80iterations 1.6533490E-02 0.4847994 at 90iterations 8.4420387E-03 0.2608032 at 100iterations 4.3462650E-03 0.1649208 at 110iterations 2.3730961E-03 8.6997986E-02 at 120iterations finished qdiffx linear iterations at : 06:11:31 total time elapsed so far: 8.210000 # loops : 120 mean,max change (kT/e) : 2.3730961E-03 8.6997986E-02 energy calculations done at 8.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.380000 DelPhi exited at 06:11:32 8.382u 0.300s 0:09.41 92.2% 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 06:11:32 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 = 2043 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: 3.169516 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): 27.06500 70.73000 ymin,ymax (A): 43.91700 82.06900 zmin,zma (A): -60.27600 -9.732000 x,y,z range (A): 43.66500 38.15200 50.54400 scale (grids/A): 3.169516 object centre (A): 48.89750 62.99300 -35.00400 number of atom coordinates read : 2043 total number of charged atoms : 1913 net assigned charge : 5.500006 assigned positive charge : 307.9621 centred at (gu) : 92.61929 87.64161 85.80685 assigned negative charge : -302.4622 centred at (gu) : 93.28754 88.01393 85.91831 start vw surface at 0.1600000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 169963 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17565 grid for indexing accessible points = 1.400000 m= 94682 mr = 125690 m= 39990 mr = 78715 m= 11959 mr = 32881 m= 2325 mr = 9244 m= 252 mr = 1639 m= 4 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.720000 number of dielectric boundary points 70879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 15304 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) : 2.113010 object centre at (A) : 48.89750 62.99300 -35.00400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2917221 -5.3090990E-02 midg,1,midg; midg,igrid,midg 0.2722336 -4.2301837E-02 1,midg,midg; igrid,midg,midg 0.3112860 0.1805706 gauss-seidel spectral radius is 0.9992938 estimated iterations to convergence 297 setup time was (sec) 1.990000 now iterating at: 06:11:34 rms-change max change #iterations 10.10129 308.3156 at 10iterations 6.015927 124.9801 at 20iterations 3.578766 71.95603 at 30iterations 2.112564 40.66201 at 40iterations 1.247539 24.52036 at 50iterations 0.7342098 13.84375 at 60iterations 0.4318782 8.234951 at 70iterations 0.2533481 4.567256 at 80iterations 0.1489653 2.934135 at 90iterations 8.7368086E-02 1.810138 at 100iterations 5.1433451E-02 0.9017577 at 110iterations 3.0459493E-02 0.6036682 at 120iterations 1.8254140E-02 0.3422852 at 130iterations 1.1155526E-02 0.2015648 at 140iterations 7.1282741E-03 0.1354914 at 150iterations 4.7917478E-03 9.7255707E-02 at 160iterations 3.4467045E-03 6.1061859E-02 at 170iterations 2.6486525E-03 4.4761658E-02 at 180iterations finished qdiffx linear iterations at : 06:11:44 total time elapsed so far: 11.42000 # loops : 180 mean,max change (kT/e) : 2.6486525E-03 4.4761658E-02 energy calculations done at 11.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.59000 DelPhi exited at 06:11:44 11.597u 0.188s 0:12.16 96.7% 0+0k 0+0io 0pf+0w