Tue Oct 11 08:25:47 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+sph2.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 = amb2.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 08:25:48 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3195 !!! WARNING: HIQ 76 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6044759 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): -11.60800 37.14800 ymin,ymax (A): -27.25600 21.31700 zmin,zma (A): -13.19500 45.69900 x,y,z range (A): 48.75600 48.57300 58.89400 scale (grids/A): 0.6044759 object centre (A): 12.77000 -2.969501 16.25200 number of atom coordinates read : 3195 total number of charged atoms : 2779 net assigned charge : -0.8459826 assigned positive charge : 447.6553 centred at (gu) : 90.17981 90.94219 92.26213 assigned negative charge : -448.5022 centred at (gu) : 90.00787 90.84428 92.14164 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6996 nv = 96 ne = 84 npr = 60445 no. pairs analyzed = 60445 no. exposed pairs = 3521 no. arc points = 24188 no. surface atoms = 1179 nbur = 2016 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3940 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 60 time to turn everything in is 0.3800000 number of dielectric boundary points 3355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2438 ## 262 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8757 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8942392E-09 8.6563201E-09 midg,1,midg; midg,igrid,midg -4.3407842E-09 5.0294404E-09 1,midg,midg; igrid,midg,midg -8.6869774E-09 7.8109812E-09 gauss-seidel spectral radius is 0.9858553 estimated iterations to convergence 69 setup time was (sec) 0.6000000 now iterating at: 08:25:48 rms-change max change #iterations 0.1184429 20.49460 at 10iterations 1.0457220E-02 1.539848 at 20iterations 9.5316779E-04 0.1442518 at 30iterations 9.2459595E-05 1.2966156E-02 at 40iterations 1.4956232E-05 1.8997192E-03 at 50iterations finished qdiffx linear iterations at : 08:25:51 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.4956232E-05 1.8997192E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 08:25:51 3.394u 0.146s 0:03.92 90.0% 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 08:25:51 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3195 !!! WARNING: HIQ 76 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.813427 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): -11.60800 37.14800 ymin,ymax (A): -27.25600 21.31700 zmin,zma (A): -13.19500 45.69900 x,y,z range (A): 48.75600 48.57300 58.89400 scale (grids/A): 1.813427 object centre (A): 12.77000 -2.969501 16.25200 number of atom coordinates read : 3195 total number of charged atoms : 2779 net assigned charge : -0.8459826 assigned positive charge : 447.6553 centred at (gu) : 90.53859 92.82570 96.78573 assigned negative charge : -448.5022 centred at (gu) : 90.02322 92.53249 96.42467 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 76262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24188 grid for indexing accessible points = 1.400000 m= 26760 mr = 53956 m= 3617 mr = 19783 m= 167 mr = 2166 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 2993 time to turn everything in is 0.6600000 number of dielectric boundary points 30857 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 21647 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) : 0.6044759 object centre at (A) : 12.77000 -2.969501 16.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5005345E-02 8.7144133E-03 midg,1,midg; midg,igrid,midg -7.7256830E-03 2.1236243E-03 1,midg,midg; igrid,midg,midg -5.9969607E-03 3.5310928E-02 gauss-seidel spectral radius is 0.9985249 estimated iterations to convergence 206 setup time was (sec) 0.9500000 now iterating at: 08:25:53 rms-change max change #iterations 4.187293 164.1893 at 10iterations 1.899245 66.11598 at 20iterations 0.8641043 30.18054 at 30iterations 0.3955891 11.82364 at 40iterations 0.1795420 5.687557 at 50iterations 8.1881106E-02 2.725668 at 60iterations 3.7306476E-02 1.297033 at 70iterations 1.6972931E-02 0.5400620 at 80iterations 7.7373330E-03 0.2392273 at 90iterations 3.5259647E-03 0.1102157 at 100iterations 1.6104573E-03 5.2165985E-02 at 110iterations 7.3338463E-04 2.4179459E-02 at 120iterations finished qdiffx linear iterations at : 08:25:59 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 7.3338463E-04 2.4179459E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 08:26:00 7.603u 0.170s 0:08.08 96.1% 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 08:26:00 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3195 !!! WARNING: HIQ 76 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.720141 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): -11.60800 37.14800 ymin,ymax (A): -27.25600 21.31700 zmin,zma (A): -13.19500 45.69900 x,y,z range (A): 48.75600 48.57300 58.89400 scale (grids/A): 2.720141 object centre (A): 12.77000 -2.969501 16.25200 number of atom coordinates read : 3195 total number of charged atoms : 2779 net assigned charge : -0.8459826 assigned positive charge : 447.6553 centred at (gu) : 90.80758 94.23837 100.1785 assigned negative charge : -448.5022 centred at (gu) : 90.03477 93.79871 99.63696 start vw surface at 0.1800000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 176685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24188 grid for indexing accessible points = 1.400000 m= 88850 mr = 130552 m= 29859 mr = 73180 m= 6420 mr = 23983 m= 757 mr = 4764 m= 26 mr = 440 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 9966 time to turn everything in is 1.400000 number of dielectric boundary points 69674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 22229 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) : 1.813427 object centre at (A) : 12.77000 -2.969501 16.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.009171 0.2862261 midg,1,midg; midg,igrid,midg -0.1002463 2.1816051E-02 1,midg,midg; igrid,midg,midg -6.0999349E-02 0.3775488 gauss-seidel spectral radius is 0.9992267 estimated iterations to convergence 284 setup time was (sec) 1.690000 now iterating at: 08:26:01 rms-change max change #iterations 10.03416 387.0330 at 10iterations 5.809107 150.2940 at 20iterations 3.342314 81.38141 at 30iterations 1.916975 38.71184 at 40iterations 1.098113 21.10145 at 50iterations 0.6261260 11.72934 at 60iterations 0.3588980 6.616420 at 70iterations 0.2041003 4.319958 at 80iterations 0.1161428 2.141811 at 90iterations 6.6061631E-02 1.185734 at 100iterations 3.7684966E-02 0.7362041 at 110iterations 2.1448614E-02 0.4030390 at 120iterations 1.2176216E-02 0.2097473 at 130iterations 6.9488157E-03 0.1269230 at 140iterations 3.9605950E-03 7.2404861E-02 at 150iterations 2.2633935E-03 4.5124531E-02 at 160iterations 1.2989941E-03 2.2470474E-02 at 170iterations 7.5012067E-04 1.3867855E-02 at 180iterations finished qdiffx linear iterations at : 08:26:12 total time elapsed so far: 12.13000 # loops : 180 mean,max change (kT/e) : 7.5012067E-04 1.3867855E-02 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 08:26:13 12.339u 0.189s 0:12.94 96.6% 0+0k 0+0io 0pf+0w