Tue Oct 11 06:09:53 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 06:09:54 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 = 2023 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: 0.7141138 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): -9.5999956E-02 46.72300 ymin,ymax (A): 0.7880000 40.65500 zmin,zma (A): -3.881000 45.97100 x,y,z range (A): 46.81900 39.86700 49.85200 scale (grids/A): 0.7141138 object centre (A): 23.31350 20.72150 21.04500 number of atom coordinates read : 2023 total number of charged atoms : 1941 net assigned charge : 7.500009 assigned positive charge : 314.1970 centred at (gu) : 90.98383 90.12100 89.83488 assigned negative charge : -306.6972 centred at (gu) : 91.14993 90.09844 89.87188 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6780 nv = 96 ne = 84 npr = 41330 no. pairs analyzed = 41330 no. exposed pairs = 2374 no. arc points = 16227 no. surface atoms = 811 nbur = 1212 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 415 mr = 3874 m= 4 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.2900000 number of dielectric boundary points 3247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1597 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7830 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8789684E-08 5.2502042E-08 midg,1,midg; midg,igrid,midg 6.0905684E-08 8.9691149E-08 1,midg,midg; igrid,midg,midg 1.3828276E-07 -2.5463317E-08 gauss-seidel spectral radius is 0.9897661 estimated iterations to convergence 80 setup time was (sec) 0.5300000 now iterating at: 06:09:54 rms-change max change #iterations 0.2033323 28.29391 at 10iterations 2.5537321E-02 3.409307 at 20iterations 3.2493786E-03 0.4944382 at 30iterations 4.1204609E-04 6.4287186E-02 at 40iterations 5.4465232E-05 7.2174072E-03 at 50iterations finished qdiffx linear iterations at : 06:09:57 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 5.4465232E-05 7.2174072E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 06:09:57 3.302u 0.146s 0:03.84 89.5% 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 06:09:57 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 = 2023 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: 2.142341 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): -9.5999956E-02 46.72300 ymin,ymax (A): 0.7880000 40.65500 zmin,zma (A): -3.881000 45.97100 x,y,z range (A): 46.81900 39.86700 49.85200 scale (grids/A): 2.142341 object centre (A): 23.31350 20.72150 21.04500 number of atom coordinates read : 2023 total number of charged atoms : 1941 net assigned charge : 7.500009 assigned positive charge : 314.1970 centred at (gu) : 92.95134 90.36303 89.50465 assigned negative charge : -306.6972 centred at (gu) : 93.45004 90.29556 89.61575 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 72043 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16227 grid for indexing accessible points = 1.400000 m= 27341 mr = 51147 m= 4987 mr = 20358 m= 516 mr = 3210 m= 14 mr = 288 m= 0 mr = 3 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 647 time to turn everything in is 0.5900000 number of dielectric boundary points 29895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 15420 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) : 0.7141138 object centre at (A) : 23.31350 20.72150 21.04500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5239579E-02 6.4648479E-02 midg,1,midg; midg,igrid,midg 5.6349626E-03 2.9460968E-02 1,midg,midg; igrid,midg,midg 4.3222096E-02 1.7856404E-02 gauss-seidel spectral radius is 0.9988393 estimated iterations to convergence 232 setup time was (sec) 0.8700000 now iterating at: 06:09:58 rms-change max change #iterations 4.650426 188.2148 at 10iterations 2.309754 72.20262 at 20iterations 1.148643 38.80211 at 30iterations 0.5732513 18.97554 at 40iterations 0.2844522 8.638966 at 50iterations 0.1418233 4.608057 at 60iterations 7.0625000E-02 2.280228 at 70iterations 3.5096690E-02 1.035545 at 80iterations 1.7510494E-02 0.5287466 at 90iterations 8.7028164E-03 0.2674046 at 100iterations 4.3337038E-03 0.1434708 at 110iterations 2.1682838E-03 6.4867020E-02 at 120iterations finished qdiffx linear iterations at : 06:10:05 total time elapsed so far: 7.200000 # loops : 120 mean,max change (kT/e) : 2.1682838E-03 6.4867020E-02 energy calculations done at 7.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.390000 DelPhi exited at 06:10:05 7.392u 0.198s 0:07.86 96.4% 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 06:10:05 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 = 2023 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: 3.213512 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): -9.5999956E-02 46.72300 ymin,ymax (A): 0.7880000 40.65500 zmin,zma (A): -3.881000 45.97100 x,y,z range (A): 46.81900 39.86700 49.85200 scale (grids/A): 3.213512 object centre (A): 23.31350 20.72150 21.04500 number of atom coordinates read : 2023 total number of charged atoms : 1941 net assigned charge : 7.500009 assigned positive charge : 314.1970 centred at (gu) : 94.42711 90.54459 89.25698 assigned negative charge : -306.6972 centred at (gu) : 95.17507 90.44334 89.42364 start vw surface at 0.1500000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 166343 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16227 grid for indexing accessible points = 1.400000 m= 86792 mr = 123160 m= 33487 mr = 71882 m= 9420 mr = 26996 m= 1935 mr = 7143 m= 260 mr = 1409 m= 15 mr = 174 m= 0 mr = 6 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 2027 time to turn everything in is 1.770000 number of dielectric boundary points 67482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 15524 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) : 2.142341 object centre at (A) : 23.31350 20.72150 21.04500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2775355 0.7439061 midg,1,midg; midg,igrid,midg 2.4211764E-02 0.2257766 1,midg,midg; igrid,midg,midg 0.3391832 0.3110740 gauss-seidel spectral radius is 0.9992929 estimated iterations to convergence 297 setup time was (sec) 2.060000 now iterating at: 06:10:08 rms-change max change #iterations 10.30995 324.9533 at 10iterations 6.113908 138.8020 at 20iterations 3.603012 85.50513 at 30iterations 2.122570 46.68407 at 40iterations 1.243974 25.31216 at 50iterations 0.7321287 15.59947 at 60iterations 0.4282169 7.675080 at 70iterations 0.2512936 5.996274 at 80iterations 0.1468928 2.968147 at 90iterations 8.5970044E-02 1.647563 at 100iterations 5.0404396E-02 0.9842205 at 110iterations 2.9472295E-02 0.5277405 at 120iterations 1.7329674E-02 0.3484344 at 130iterations 1.0220720E-02 0.1803732 at 140iterations 6.0834498E-03 0.1129570 at 150iterations 3.6686368E-03 6.9206238E-02 at 160iterations 2.2711484E-03 4.5465469E-02 at 170iterations 1.4556452E-03 2.7406693E-02 at 180iterations finished qdiffx linear iterations at : 06:10:18 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 1.4556452E-03 2.7406693E-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 06:10:18 12.256u 0.175s 0:13.10 94.8% 0+0k 0+0io 0pf+0w