Tue Oct 11 08:33:50 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 08:33:51 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2894 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6594669 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): -15.42400 34.53200 ymin,ymax (A): 7.009000 55.27600 zmin,zma (A): 26.12100 80.10400 x,y,z range (A): 49.95600 48.26700 53.98300 scale (grids/A): 0.6594669 object centre (A): 9.554001 31.14250 53.11250 number of atom coordinates read : 2894 total number of charged atoms : 2741 net assigned charge : 2.162016 assigned positive charge : 439.0515 centred at (gu) : 89.88112 90.43800 88.92947 assigned negative charge : -436.8902 centred at (gu) : 90.13202 90.32715 88.92928 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8462 nv = 96 ne = 84 npr = 59299 no. pairs analyzed = 59299 no. exposed pairs = 3576 no. arc points = 24275 no. surface atoms = 1197 nbur = 1697 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 462 mr = 4851 m= 2 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3800000 number of dielectric boundary points 4015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2418 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10034 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5397758E-09 4.3218273E-09 midg,1,midg; midg,igrid,midg -1.7573976E-08 3.2200500E-08 1,midg,midg; igrid,midg,midg 6.0447519E-08 -4.9978755E-08 gauss-seidel spectral radius is 0.9881055 estimated iterations to convergence 75 setup time was (sec) 0.6600000 now iterating at: 08:33:51 rms-change max change #iterations 0.1738612 22.17157 at 10iterations 1.8995894E-02 2.590052 at 20iterations 2.1374116E-03 0.3079882 at 30iterations 2.8860295E-04 3.7712097E-02 at 40iterations 6.3126463E-05 7.8201294E-03 at 50iterations finished qdiffx linear iterations at : 08:33:55 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 6.3126463E-05 7.8201294E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 08:33:56 4.206u 0.292s 0:05.19 86.5% 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 08:33:56 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2894 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.978401 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): -15.42400 34.53200 ymin,ymax (A): 7.009000 55.27600 zmin,zma (A): 26.12100 80.10400 x,y,z range (A): 49.95600 48.26700 53.98300 scale (grids/A): 1.978401 object centre (A): 9.554001 31.14250 53.11250 number of atom coordinates read : 2894 total number of charged atoms : 2741 net assigned charge : 2.162016 assigned positive charge : 439.0515 centred at (gu) : 89.64282 91.31353 86.78766 assigned negative charge : -436.8902 centred at (gu) : 90.39592 90.98118 86.78768 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 90603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24275 grid for indexing accessible points = 1.400000 m= 34688 mr = 64603 m= 5717 mr = 25958 m= 363 mr = 3622 m= 8 mr = 142 m= 0 mr = 2 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 1300 time to turn everything in is 0.7800000 number of dielectric boundary points 37052 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 21651 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) : 0.6594669 object centre at (A) : 9.554001 31.14250 53.11250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1552860E-03 -2.0216020E-02 midg,1,midg; midg,igrid,midg -1.0936484E-02 1.8229121E-02 1,midg,midg; igrid,midg,midg 7.8636296E-02 -1.0257310E-02 gauss-seidel spectral radius is 0.9987583 estimated iterations to convergence 225 setup time was (sec) 1.070000 now iterating at: 08:33:57 rms-change max change #iterations 4.886477 193.1559 at 10iterations 2.381232 76.49115 at 20iterations 1.151196 33.91512 at 30iterations 0.5613188 15.27252 at 40iterations 0.2728583 8.132442 at 50iterations 0.1324510 3.670446 at 60iterations 6.4385265E-02 1.804996 at 70iterations 3.1356126E-02 0.9405718 at 80iterations 1.5276276E-02 0.4300973 at 90iterations 7.4366811E-03 0.2258148 at 100iterations 3.6277410E-03 9.9891663E-02 at 110iterations 1.7819727E-03 5.1670074E-02 at 120iterations finished qdiffx linear iterations at : 08:34:06 total time elapsed so far: 9.700000 # loops : 120 mean,max change (kT/e) : 1.7819727E-03 5.1670074E-02 energy calculations done at 9.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.890000 DelPhi exited at 08:34:07 9.889u 0.338s 0:11.04 92.4% 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 08:34:07 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2894 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.967601 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): -15.42400 34.53200 ymin,ymax (A): 7.009000 55.27600 zmin,zma (A): 26.12100 80.10400 x,y,z range (A): 49.95600 48.26700 53.98300 scale (grids/A): 2.967601 object centre (A): 9.554001 31.14250 53.11250 number of atom coordinates read : 2894 total number of charged atoms : 2741 net assigned charge : 2.162016 assigned positive charge : 439.0515 centred at (gu) : 89.46415 91.97025 85.18130 assigned negative charge : -436.8902 centred at (gu) : 90.59379 91.47183 85.18144 start vw surface at 0.1800000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 209498 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24275 grid for indexing accessible points = 1.400000 m= 111045 mr = 155646 m= 41418 mr = 92169 m= 10279 mr = 33683 m= 1546 mr = 7701 m= 114 mr = 1019 m= 4 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 4385 time to turn everything in is 2.110000 number of dielectric boundary points 83630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.280000 number of grid points assigned charge 21928 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) : 1.978401 object centre at (A) : 9.554001 31.14250 53.11250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1258255 -0.3086006 midg,1,midg; midg,igrid,midg -0.1392367 0.2403722 1,midg,midg; igrid,midg,midg 0.6726201 -6.1735980E-02 gauss-seidel spectral radius is 0.9992928 estimated iterations to convergence 297 setup time was (sec) 2.460000 now iterating at: 08:34:10 rms-change max change #iterations 11.23213 414.1980 at 10iterations 6.624544 142.5849 at 20iterations 3.909129 74.48999 at 30iterations 2.296993 43.98379 at 40iterations 1.349390 26.06115 at 50iterations 0.7911174 13.64863 at 60iterations 0.4633555 8.109881 at 70iterations 0.2710050 4.389816 at 80iterations 0.1584580 2.898556 at 90iterations 9.2612229E-02 1.508136 at 100iterations 5.4027453E-02 0.9567580 at 110iterations 3.1606320E-02 0.5378189 at 120iterations 1.8430911E-02 0.3039253 at 130iterations 1.0787359E-02 0.1863480 at 140iterations 6.3279304E-03 0.1239719 at 150iterations 3.7252645E-03 6.1509609E-02 at 160iterations 2.2047104E-03 3.8360596E-02 at 170iterations 1.3214815E-03 2.4615288E-02 at 180iterations finished qdiffx linear iterations at : 08:34:24 total time elapsed so far: 16.92000 # loops : 180 mean,max change (kT/e) : 1.3214815E-03 2.4615288E-02 energy calculations done at 16.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.11000 DelPhi exited at 08:34:25 17.110u 0.321s 0:18.20 95.7% 0+0k 0+0io 0pf+0w