Tue Oct 11 08:17:28 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 Tue Oct 11 2011 at 08:17:28 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2707 !!! WARNING: FMN 398 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6652713 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): -24.95800 21.60200 ymin,ymax (A): -64.13300 -10.62100 zmin,zma (A): -17.27200 30.25200 x,y,z range (A): 46.56000 53.51200 47.52400 scale (grids/A): 0.6652713 object centre (A): -1.678000 -37.37700 6.490001 number of atom coordinates read : 2707 total number of charged atoms : 2579 net assigned charge : 4.000021 assigned positive charge : 415.9824 centred at (gu) : 90.74207 89.95648 90.46462 assigned negative charge : -411.9834 centred at (gu) : 90.58234 90.19150 90.48228 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8190 nv = 96 ne = 84 npr = 55156 no. pairs analyzed = 55156 no. exposed pairs = 3363 no. arc points = 22785 no. surface atoms = 1129 nbur = 1578 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 494 mr = 4707 m= 4 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3700000 number of dielectric boundary points 3914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2100 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9477 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4318890E-08 7.9175715E-09 midg,1,midg; midg,igrid,midg 6.7159682E-08 -4.5939391E-08 1,midg,midg; igrid,midg,midg -2.3456547E-08 5.7462675E-08 gauss-seidel spectral radius is 0.9882985 estimated iterations to convergence 75 setup time was (sec) 0.6900000 now iterating at: 08:17:29 rms-change max change #iterations 0.1791399 24.42850 at 10iterations 2.0303668E-02 2.657484 at 20iterations 3.2662654E-03 0.6335297 at 30iterations 9.6389739E-04 0.1998444 at 40iterations 3.5196095E-04 7.4775696E-02 at 50iterations finished qdiffx linear iterations at : 08:17:33 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 3.5196095E-04 7.4775696E-02 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 08:17:33 4.429u 0.277s 0:05.16 90.8% 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 08:17:33 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2707 !!! WARNING: FMN 398 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.995814 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): -24.95800 21.60200 ymin,ymax (A): -64.13300 -10.62100 zmin,zma (A): -17.27200 30.25200 x,y,z range (A): 46.56000 53.51200 47.52400 scale (grids/A): 1.995814 object centre (A): -1.678000 -37.37700 6.490001 number of atom coordinates read : 2707 total number of charged atoms : 2579 net assigned charge : 4.000021 assigned positive charge : 415.9824 centred at (gu) : 92.22566 89.86877 91.39326 assigned negative charge : -411.9834 centred at (gu) : 91.74660 90.57417 91.44653 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22785 grid for indexing accessible points = 1.400000 m= 33070 mr = 62410 m= 5536 mr = 24836 m= 379 mr = 3589 m= 3 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1307 time to turn everything in is 0.6500000 number of dielectric boundary points 35919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20394 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) : 0.6652713 object centre at (A) : -1.678000 -37.37700 6.490001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7465742E-02 -2.3228800E-02 midg,1,midg; midg,igrid,midg 7.3461965E-02 -4.9565773E-02 1,midg,midg; igrid,midg,midg -1.6138334E-02 5.2695587E-02 gauss-seidel spectral radius is 0.9987667 estimated iterations to convergence 225 setup time was (sec) 0.9800000 now iterating at: 08:17:34 rms-change max change #iterations 4.801265 171.9328 at 10iterations 2.332341 71.02457 at 20iterations 1.133636 33.84200 at 30iterations 0.5504770 15.11893 at 40iterations 0.2687203 7.693905 at 50iterations 0.1308671 3.549209 at 60iterations 6.3847773E-02 1.766300 at 70iterations 3.1397503E-02 0.9247684 at 80iterations 1.5562454E-02 0.5069542 at 90iterations 7.9177003E-03 0.2628479 at 100iterations 4.2036646E-03 0.1526260 at 110iterations 2.3801539E-03 9.1087341E-02 at 120iterations finished qdiffx linear iterations at : 08:17:43 total time elapsed so far: 9.520000 # loops : 120 mean,max change (kT/e) : 2.3801539E-03 9.1087341E-02 energy calculations done at 9.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.700000 DelPhi exited at 08:17:44 9.701u 0.260s 0:10.32 96.5% 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 08:17:44 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2707 !!! WARNING: FMN 398 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.993721 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): -24.95800 21.60200 ymin,ymax (A): -64.13300 -10.62100 zmin,zma (A): -17.27200 30.25200 x,y,z range (A): 46.56000 53.51200 47.52400 scale (grids/A): 2.993721 object centre (A): -1.678000 -37.37700 6.490001 number of atom coordinates read : 2707 total number of charged atoms : 2579 net assigned charge : 4.000021 assigned positive charge : 415.9824 centred at (gu) : 93.33835 89.80288 92.08970 assigned negative charge : -411.9834 centred at (gu) : 92.61986 90.86112 92.16977 start vw surface at 0.1800000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 203421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22785 grid for indexing accessible points = 1.400000 m= 105540 mr = 150954 m= 40089 mr = 87415 m= 10144 mr = 32730 m= 1633 mr = 7661 m= 95 mr = 1119 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 4089 time to turn everything in is 1.860000 number of dielectric boundary points 81010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 20632 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) : 1.995814 object centre at (A) : -1.678000 -37.37700 6.490001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2464204 -0.2742350 midg,1,midg; midg,igrid,midg 1.004024 -0.7687887 1,midg,midg; igrid,midg,midg -0.1692067 0.4194670 gauss-seidel spectral radius is 0.9992917 estimated iterations to convergence 296 setup time was (sec) 2.210000 now iterating at: 08:17:46 rms-change max change #iterations 11.08416 492.7638 at 10iterations 6.511499 137.8615 at 20iterations 3.832092 73.83249 at 30iterations 2.248581 41.19219 at 40iterations 1.316124 22.03497 at 50iterations 0.7710903 12.46811 at 60iterations 0.4509066 8.029385 at 70iterations 0.2630894 4.957375 at 80iterations 0.1536857 2.623567 at 90iterations 8.9649744E-02 1.619827 at 100iterations 5.2418310E-02 0.9674606 at 110iterations 3.0728694E-02 0.6344261 at 120iterations 1.8060355E-02 0.3896790 at 130iterations 1.0734636E-02 0.2311630 at 140iterations 6.5160249E-03 0.1414528 at 150iterations 4.0836819E-03 9.2914581E-02 at 160iterations 2.6955872E-03 6.1634064E-02 at 170iterations 1.9010364E-03 4.5364380E-02 at 180iterations finished qdiffx linear iterations at : 08:18:00 total time elapsed so far: 15.92000 # loops : 180 mean,max change (kT/e) : 1.9010364E-03 4.5364380E-02 energy calculations done at 15.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.10000 DelPhi exited at 08:18:01 16.104u 0.277s 0:17.02 96.1% 0+0k 0+0io 0pf+0w