Sun Oct 9 13:21:43 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 Sun Oct 9 2011 at 13:21:43 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 = 2367 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: 0.6699538 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): -7.141000 44.64600 ymin,ymax (A): 22.17600 75.31400 zmin,zma (A): 41.59200 84.03200 x,y,z range (A): 51.78700 53.13799 42.44000 scale (grids/A): 0.6699538 object centre (A): 18.75250 48.74500 62.81200 number of atom coordinates read : 2367 total number of charged atoms : 2226 net assigned charge : 4.500020 assigned positive charge : 361.9960 centred at (gu) : 89.80791 90.41830 90.54245 assigned negative charge : -357.4966 centred at (gu) : 89.77465 90.59367 90.64809 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7215 nv = 96 ne = 84 npr = 47005 no. pairs analyzed = 47005 no. exposed pairs = 2961 no. arc points = 21187 no. surface atoms = 995 nbur = 1372 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 423 mr = 3941 m= 5 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2141 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8360 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5625295E-08 -1.0972381E-08 midg,1,midg; midg,igrid,midg 5.1072082E-08 -2.9034684E-08 1,midg,midg; igrid,midg,midg 7.7865776E-09 2.2215779E-08 gauss-seidel spectral radius is 0.9884301 estimated iterations to convergence 76 setup time was (sec) 0.5200000 now iterating at: 13:21:43 rms-change max change #iterations 0.1650567 23.73153 at 10iterations 1.8629696E-02 2.710350 at 20iterations 2.3896110E-03 0.4105301 at 30iterations 5.1150750E-04 8.5083008E-02 at 40iterations 1.5776126E-04 2.9064178E-02 at 50iterations finished qdiffx linear iterations at : 13:21:46 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 1.5776126E-04 2.9064178E-02 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 13:21:46 3.312u 0.154s 0:03.75 92.2% 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 Sun Oct 9 2011 at 13:21:46 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 = 2367 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: 2.009861 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): -7.141000 44.64600 ymin,ymax (A): 22.17600 75.31400 zmin,zma (A): 41.59200 84.03200 x,y,z range (A): 51.78700 53.13799 42.44000 scale (grids/A): 2.009861 object centre (A): 18.75250 48.74500 62.81200 number of atom coordinates read : 2367 total number of charged atoms : 2226 net assigned charge : 4.500020 assigned positive charge : 361.9960 centred at (gu) : 89.42316 91.25462 91.62693 assigned negative charge : -357.4966 centred at (gu) : 89.32377 91.78085 91.94392 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 76680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21187 grid for indexing accessible points = 1.400000 m= 29114 mr = 52910 m= 5113 mr = 21649 m= 421 mr = 3267 m= 9 mr = 188 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 33323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 17624 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) : 0.6699538 object centre at (A) : 18.75250 48.74500 62.81200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7134839E-02 -1.7409193E-03 midg,1,midg; midg,igrid,midg 1.6602989E-02 -4.3320443E-02 1,midg,midg; igrid,midg,midg 5.0022561E-02 1.4569533E-02 gauss-seidel spectral radius is 0.9987510 estimated iterations to convergence 224 setup time was (sec) 0.8700000 now iterating at: 13:21:47 rms-change max change #iterations 4.480294 281.7095 at 10iterations 2.152189 83.52478 at 20iterations 1.047447 34.96260 at 30iterations 0.5041367 16.30722 at 40iterations 0.2442976 7.626924 at 50iterations 0.1186417 3.751904 at 60iterations 5.7548821E-02 1.740021 at 70iterations 2.7921187E-02 0.8672791 at 80iterations 1.3636566E-02 0.4525902 at 90iterations 6.7129568E-03 0.2108765 at 100iterations 3.3459496E-03 0.1091213 at 110iterations 1.7177890E-03 5.7807922E-02 at 120iterations finished qdiffx linear iterations at : 13:21:54 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 1.7177890E-03 5.7807922E-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) 7.580000 DelPhi exited at 13:21:55 7.580u 0.196s 0:08.05 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 Sun Oct 9 2011 at 13:21:55 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 = 2367 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: 3.014792 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): -7.141000 44.64600 ymin,ymax (A): 22.17600 75.31400 zmin,zma (A): 41.59200 84.03200 x,y,z range (A): 51.78700 53.13799 42.44000 scale (grids/A): 3.014792 object centre (A): 18.75250 48.74500 62.81200 number of atom coordinates read : 2367 total number of charged atoms : 2226 net assigned charge : 4.500020 assigned positive charge : 361.9960 centred at (gu) : 89.13468 91.88176 92.44034 assigned negative charge : -357.4966 centred at (gu) : 88.98569 92.67126 92.91587 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 176637 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21187 grid for indexing accessible points = 1.400000 m= 92200 mr = 127904 m= 35539 mr = 75426 m= 9588 mr = 28863 m= 1742 mr = 7236 m= 161 mr = 1236 m= 2 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.520000 number of dielectric boundary points 75130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 17808 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) : 2.009861 object centre at (A) : 18.75250 48.74500 62.81200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4629282 -0.1175614 midg,1,midg; midg,igrid,midg 0.3338199 -0.5142589 1,midg,midg; igrid,midg,midg 0.7018809 -3.3019215E-02 gauss-seidel spectral radius is 0.9992803 estimated iterations to convergence 294 setup time was (sec) 1.820000 now iterating at: 13:21:57 rms-change max change #iterations 10.28642 397.0383 at 10iterations 6.057531 148.0535 at 20iterations 3.565897 75.89945 at 30iterations 2.087565 40.23564 at 40iterations 1.220144 22.80167 at 50iterations 0.7145082 13.98622 at 60iterations 0.4163065 8.038567 at 70iterations 0.2425605 4.593298 at 80iterations 0.1412449 2.604675 at 90iterations 8.2158133E-02 1.858223 at 100iterations 4.7887020E-02 0.8826370 at 110iterations 2.8005520E-02 0.5198135 at 120iterations 1.6398275E-02 0.3279610 at 130iterations 9.7380048E-03 0.1730514 at 140iterations 5.8832993E-03 0.1106339 at 150iterations 3.6728254E-03 7.3772430E-02 at 160iterations 2.4072398E-03 5.6396484E-02 at 170iterations 1.6787075E-03 3.8589478E-02 at 180iterations finished qdiffx linear iterations at : 13:22:07 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 1.6787075E-03 3.8589478E-02 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 13:22:07 12.250u 0.191s 0:12.69 98.0% 0+0k 0+0io 0pf+0w