Sat Oct 8 14:20:08 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 14:20:08 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3023 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6399080 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): -12.03200 43.60100 ymin,ymax (A): -22.24500 22.66500 zmin,zma (A): -8.303000 46.92000 x,y,z range (A): 55.63300 44.91000 55.22300 scale (grids/A): 0.6399080 object centre (A): 15.78450 0.2099991 19.30850 number of atom coordinates read : 3023 total number of charged atoms : 2876 net assigned charge : 7.1674585E-06 assigned positive charge : 452.4766 centred at (gu) : 88.72743 89.46038 92.10656 assigned negative charge : -452.4773 centred at (gu) : 88.72466 89.37206 92.02603 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8259 nv = 96 ne = 84 npr = 63429 no. pairs analyzed = 63429 no. exposed pairs = 3456 no. arc points = 23893 no. surface atoms = 1174 nbur = 1849 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 4843 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2300 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9957 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0585955E-09 1.6866935E-08 midg,1,midg; midg,igrid,midg -1.3716005E-08 1.0331635E-08 1,midg,midg; igrid,midg,midg -7.1967832E-10 1.5523217E-10 gauss-seidel spectral radius is 0.9873779 estimated iterations to convergence 73 setup time was (sec) 0.6700000 now iterating at: 14:20:09 rms-change max change #iterations 0.1587490 20.47533 at 10iterations 1.6176695E-02 2.180882 at 20iterations 1.6944229E-03 0.2233610 at 30iterations 2.1235191E-04 3.0866623E-02 at 40iterations 3.5107551E-05 5.2013397E-03 at 50iterations finished qdiffx linear iterations at : 14:20:13 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 3.5107551E-05 5.2013397E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 14:20:13 4.164u 0.266s 0:04.73 93.4% 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 14:20:13 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3023 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.919724 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): -12.03200 43.60100 ymin,ymax (A): -22.24500 22.66500 zmin,zma (A): -8.303000 46.92000 x,y,z range (A): 55.63300 44.91000 55.22300 scale (grids/A): 1.919724 object centre (A): 15.78450 0.2099991 19.30850 number of atom coordinates read : 3023 total number of charged atoms : 2876 net assigned charge : 7.1674585E-06 assigned positive charge : 452.4766 centred at (gu) : 86.18143 88.38056 96.31931 assigned negative charge : -452.4773 centred at (gu) : 86.17370 88.11584 96.07786 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 89298 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23893 grid for indexing accessible points = 1.400000 m= 32914 mr = 64749 m= 5071 mr = 24766 m= 282 mr = 3113 m= 6 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 34857 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 22674 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) : 0.6399080 object centre at (A) : 15.78450 0.2099991 19.30850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8669277E-02 2.8548684E-02 midg,1,midg; midg,igrid,midg -4.3385685E-04 1.7873704E-02 1,midg,midg; igrid,midg,midg -4.2105485E-02 3.6922654E-03 gauss-seidel spectral radius is 0.9986880 estimated iterations to convergence 219 setup time was (sec) 1.070000 now iterating at: 14:20:15 rms-change max change #iterations 4.697862 175.8143 at 10iterations 2.248439 67.54140 at 20iterations 1.070241 32.79102 at 30iterations 0.5099037 15.72451 at 40iterations 0.2427283 6.623149 at 50iterations 0.1157107 3.259676 at 60iterations 5.5052288E-02 1.560086 at 70iterations 2.6255641E-02 0.7583294 at 80iterations 1.2523635E-02 0.3384705 at 90iterations 5.9458767E-03 0.1682715 at 100iterations 2.8432773E-03 7.9111457E-02 at 110iterations 1.3574704E-03 3.7170410E-02 at 120iterations finished qdiffx linear iterations at : 14:20:23 total time elapsed so far: 9.550000 # loops : 120 mean,max change (kT/e) : 1.3574704E-03 3.7170410E-02 energy calculations done at 9.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.730000 DelPhi exited at 14:20:24 9.736u 0.319s 0:10.32 97.2% 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 Sat Oct 8 2011 at 14:20:24 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3023 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.879586 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): -12.03200 43.60100 ymin,ymax (A): -22.24500 22.66500 zmin,zma (A): -8.303000 46.92000 x,y,z range (A): 55.63300 44.91000 55.22300 scale (grids/A): 2.879586 object centre (A): 15.78450 0.2099991 19.30850 number of atom coordinates read : 3023 total number of charged atoms : 2876 net assigned charge : 7.1674585E-06 assigned positive charge : 452.4766 centred at (gu) : 84.27206 87.57072 99.47868 assigned negative charge : -452.4773 centred at (gu) : 84.26048 87.17368 99.11683 start vw surface at 0.1700000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 206933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23893 grid for indexing accessible points = 1.400000 m= 107420 mr = 156341 m= 38439 mr = 89638 m= 9185 mr = 31237 m= 1281 mr = 6815 m= 70 mr = 783 m= 0 mr = 16 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.050000 number of dielectric boundary points 78498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.210000 number of grid points assigned charge 23006 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) : 1.919724 object centre at (A) : 15.78450 0.2099991 19.30850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6007379E-02 0.5726174 midg,1,midg; midg,igrid,midg 1.3933010E-02 0.2054279 1,midg,midg; igrid,midg,midg -0.7420737 0.1107153 gauss-seidel spectral radius is 0.9992785 estimated iterations to convergence 294 setup time was (sec) 2.390000 now iterating at: 14:20:26 rms-change max change #iterations 10.98374 452.6566 at 10iterations 6.464252 138.7144 at 20iterations 3.773428 76.99210 at 30iterations 2.207167 41.78807 at 40iterations 1.285072 26.40488 at 50iterations 0.7488056 13.03402 at 60iterations 0.4349874 7.780250 at 70iterations 0.2526764 4.960675 at 80iterations 0.1466699 2.423628 at 90iterations 8.5066915E-02 1.450461 at 100iterations 4.9313691E-02 0.7639771 at 110iterations 2.8562158E-02 0.4824333 at 120iterations 1.6591979E-02 0.2801857 at 130iterations 9.6256053E-03 0.1703191 at 140iterations 5.5864649E-03 9.3133330E-02 at 150iterations 3.2524010E-03 5.7170391E-02 at 160iterations 1.9018919E-03 3.0522108E-02 at 170iterations 1.1161671E-03 1.7566204E-02 at 180iterations finished qdiffx linear iterations at : 14:20:40 total time elapsed so far: 16.47000 # loops : 180 mean,max change (kT/e) : 1.1161671E-03 1.7566204E-02 energy calculations done at 16.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.65000 DelPhi exited at 14:20:41 16.652u 0.312s 0:17.24 98.3% 0+0k 0+0io 0pf+0w