Tue Oct 11 01:13:14 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 01:13:14 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 = 2606 !!! WARNING: ASP 298 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6316200 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): 13.93800 70.30100 ymin,ymax (A): -10.99300 43.70800 zmin,zma (A): -17.43400 25.18200 x,y,z range (A): 56.36300 54.70100 42.61600 scale (grids/A): 0.6316200 object centre (A): 42.11950 16.35750 3.874000 number of atom coordinates read : 2606 total number of charged atoms : 2464 net assigned charge : 4.500018 assigned positive charge : 390.2978 centred at (gu) : 91.23558 89.51482 90.19330 assigned negative charge : -385.7984 centred at (gu) : 90.93095 89.69529 90.01866 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6945 nv = 96 ne = 84 npr = 53018 no. pairs analyzed = 53018 no. exposed pairs = 3039 no. arc points = 21304 no. surface atoms = 1030 nbur = 1576 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 334 mr = 3979 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 153 time to turn everything in is 0.3100000 number of dielectric boundary points 3265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2142 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8477 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1184382E-08 2.1327946E-08 midg,1,midg; midg,igrid,midg 2.3308498E-08 -1.0973752E-08 1,midg,midg; igrid,midg,midg -1.8458621E-08 4.1735905E-08 gauss-seidel spectral radius is 0.9870136 estimated iterations to convergence 72 setup time was (sec) 0.5500000 now iterating at: 01:13:15 rms-change max change #iterations 0.1381594 21.47202 at 10iterations 1.3713749E-02 2.283066 at 20iterations 1.7074284E-03 0.3381042 at 30iterations 3.5158696E-04 7.7175140E-02 at 40iterations 9.2556023E-05 2.1404266E-02 at 50iterations finished qdiffx linear iterations at : 01:13:18 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 9.2556023E-05 2.1404266E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 01:13:18 3.327u 0.171s 0:04.04 86.3% 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 01:13:18 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 = 2606 !!! WARNING: ASP 298 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: 1.894860 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): 13.93800 70.30100 ymin,ymax (A): -10.99300 43.70800 zmin,zma (A): -17.43400 25.18200 x,y,z range (A): 56.36300 54.70100 42.61600 scale (grids/A): 1.894860 object centre (A): 42.11950 16.35750 3.874000 number of atom coordinates read : 2606 total number of charged atoms : 2464 net assigned charge : 4.500018 assigned positive charge : 390.2978 centred at (gu) : 93.70596 88.54371 90.57944 assigned negative charge : -385.7984 centred at (gu) : 92.79272 89.08572 90.05562 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75999 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21304 grid for indexing accessible points = 1.400000 m= 26940 mr = 54149 m= 4162 mr = 20295 m= 212 mr = 2736 m= 0 mr = 74 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 4443 time to turn everything in is 0.5300000 number of dielectric boundary points 30059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19396 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) : 0.6316200 object centre at (A) : 42.11950 16.35750 3.874000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4042511E-03 3.5082806E-02 midg,1,midg; midg,igrid,midg 4.7032632E-02 -3.0552873E-02 1,midg,midg; igrid,midg,midg -7.3946230E-02 5.6683724E-03 gauss-seidel spectral radius is 0.9986193 estimated iterations to convergence 213 setup time was (sec) 0.8000000 now iterating at: 01:13:19 rms-change max change #iterations 4.199794 197.7333 at 10iterations 1.954039 64.13815 at 20iterations 0.9104273 29.08084 at 30iterations 0.4252644 13.96793 at 40iterations 0.1991435 6.058563 at 50iterations 9.2552699E-02 2.964008 at 60iterations 4.3624252E-02 1.336233 at 70iterations 2.0386733E-02 0.6349258 at 80iterations 9.6000284E-03 0.2896633 at 90iterations 4.5923172E-03 0.1652985 at 100iterations 2.2356280E-03 7.8563690E-02 at 110iterations 1.1405343E-03 4.5143127E-02 at 120iterations finished qdiffx linear iterations at : 01:13:26 total time elapsed so far: 7.110000 # loops : 120 mean,max change (kT/e) : 1.1405343E-03 4.5143127E-02 energy calculations done at 7.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 01:13:26 7.295u 0.210s 0:08.01 93.6% 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 01:13:26 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 = 2606 !!! WARNING: ASP 298 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: 2.842290 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): 13.93800 70.30100 ymin,ymax (A): -10.99300 43.70800 zmin,zma (A): -17.43400 25.18200 x,y,z range (A): 56.36300 54.70100 42.61600 scale (grids/A): 2.842290 object centre (A): 42.11950 16.35750 3.874000 number of atom coordinates read : 2606 total number of charged atoms : 2464 net assigned charge : 4.500018 assigned positive charge : 390.2978 centred at (gu) : 95.55884 87.81539 90.86915 assigned negative charge : -385.7984 centred at (gu) : 94.18889 88.62852 90.08341 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 176000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21304 grid for indexing accessible points = 1.400000 m= 88754 mr = 130788 m= 30962 mr = 73803 m= 7400 mr = 25298 m= 976 mr = 5718 m= 36 mr = 675 m= 0 mr = 8 time to grow re-entrant surface = 0.7599999 no. cavity mid-points inaccessible to solvent = 14791 time to turn everything in is 1.340000 number of dielectric boundary points 67838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 19712 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) : 1.894860 object centre at (A) : 42.11950 16.35750 3.874000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0864469E-02 0.3519151 midg,1,midg; midg,igrid,midg 0.6259771 -0.7229432 1,midg,midg; igrid,midg,midg -0.7938142 -6.1882559E-02 gauss-seidel spectral radius is 0.9992510 estimated iterations to convergence 288 setup time was (sec) 1.630000 now iterating at: 01:13:28 rms-change max change #iterations 9.795818 427.8034 at 10iterations 5.677817 131.1438 at 20iterations 3.270560 59.80869 at 30iterations 1.885824 35.35316 at 40iterations 1.081255 21.27412 at 50iterations 0.6203106 10.91258 at 60iterations 0.3563218 6.383993 at 70iterations 0.2039500 4.107224 at 80iterations 0.1169261 2.237209 at 90iterations 6.6928424E-02 1.265793 at 100iterations 3.8418785E-02 0.6970444 at 110iterations 2.2023750E-02 0.4509277 at 120iterations 1.2683198E-02 0.2330818 at 130iterations 7.3433258E-03 0.1412802 at 140iterations 4.2904811E-03 8.7245941E-02 at 150iterations 2.5362568E-03 5.1078796E-02 at 160iterations 1.5506191E-03 3.6443710E-02 at 170iterations 9.8955655E-04 2.3473740E-02 at 180iterations finished qdiffx linear iterations at : 01:13:41 total time elapsed so far: 14.23000 # loops : 180 mean,max change (kT/e) : 9.8955655E-04 2.3473740E-02 energy calculations done at 14.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.41000 DelPhi exited at 01:13:42 14.408u 0.228s 0:15.19 96.2% 0+0k 0+0io 0pf+0w