Mon Oct 10 09:44:04 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 Mon Oct 10 2011 at 09:44:04 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2889 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5759213 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): 111.1450 172.9590 ymin,ymax (A): -43.87000 10.82100 zmin,zma (A): 48.96400 101.9140 x,y,z range (A): 61.81400 54.69100 52.95000 scale (grids/A): 0.5759213 object centre (A): 142.0520 -16.52450 75.43900 number of atom coordinates read : 2889 total number of charged atoms : 2740 net assigned charge : 5.500018 assigned positive charge : 422.6028 centred at (gu) : 90.04647 89.27942 88.98544 assigned negative charge : -417.1034 centred at (gu) : 90.11626 89.32220 88.81834 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6578 nv = 96 ne = 84 npr = 55999 no. pairs analyzed = 55999 no. exposed pairs = 4451 no. arc points = 32086 no. surface atoms = 1475 nbur = 1414 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 310 mr = 2864 m= 0 mr = 19 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 4005 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3089 ## 330 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8165 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5677975E-09 3.1671457E-09 midg,1,midg; midg,igrid,midg 2.1769473E-09 2.5886160E-10 1,midg,midg; igrid,midg,midg 2.2932012E-09 -1.9686031E-10 gauss-seidel spectral radius is 0.9844530 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 09:44:05 rms-change max change #iterations 9.2293665E-02 14.38569 at 10iterations 6.8837022E-03 1.139372 at 20iterations 5.2197155E-04 8.9791536E-02 at 30iterations 4.6831356E-05 6.9351196E-03 at 40iterations 6.1282281E-06 6.9046021E-04 at 50iterations finished qdiffx linear iterations at : 09:44:08 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 6.1282281E-06 6.9046021E-04 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 09:44:09 3.486u 0.199s 0:04.29 85.5% 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 Mon Oct 10 2011 at 09:44:09 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2889 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.727764 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): 111.1450 172.9590 ymin,ymax (A): -43.87000 10.82100 zmin,zma (A): 48.96400 101.9140 x,y,z range (A): 61.81400 54.69100 52.95000 scale (grids/A): 1.727764 object centre (A): 142.0520 -16.52450 75.43900 number of atom coordinates read : 2889 total number of charged atoms : 2740 net assigned charge : 5.500018 assigned positive charge : 422.6028 centred at (gu) : 90.13924 87.83780 86.95598 assigned negative charge : -417.1034 centred at (gu) : 90.34848 87.96626 86.45461 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69709 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32086 grid for indexing accessible points = 1.400000 m= 22184 mr = 42479 m= 2850 mr = 14035 m= 108 mr = 1236 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 37099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 277 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 21281 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) : 0.5759213 object centre at (A) : 142.0520 -16.52450 75.43900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2271835E-03 2.3676345E-02 midg,1,midg; midg,igrid,midg 7.8732278E-03 6.7491154E-03 1,midg,midg; igrid,midg,midg 1.5024167E-02 2.2292817E-03 gauss-seidel spectral radius is 0.9984056 estimated iterations to convergence 199 setup time was (sec) 0.5800000 now iterating at: 09:44:09 rms-change max change #iterations 3.653760 162.3394 at 10iterations 1.604597 68.07654 at 20iterations 0.7064983 25.65021 at 30iterations 0.3110834 11.80608 at 40iterations 0.1367019 4.589907 at 50iterations 5.9887853E-02 2.140697 at 60iterations 2.6369724E-02 0.9518547 at 70iterations 1.1601019E-02 0.4334726 at 80iterations 5.0930874E-03 0.1966705 at 90iterations 2.2476050E-03 8.6236954E-02 at 100iterations 9.9073409E-04 3.8907051E-02 at 110iterations 4.3583111E-04 1.4637947E-02 at 120iterations finished qdiffx linear iterations at : 09:44:17 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 4.3583111E-04 1.4637947E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 09:44:17 7.897u 0.469s 0:08.71 95.8% 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 Mon Oct 10 2011 at 09:44:17 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2889 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.591646 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): 111.1450 172.9590 ymin,ymax (A): -43.87000 10.82100 zmin,zma (A): 48.96400 101.9140 x,y,z range (A): 61.81400 54.69100 52.95000 scale (grids/A): 2.591646 object centre (A): 142.0520 -16.52450 75.43900 number of atom coordinates read : 2889 total number of charged atoms : 2740 net assigned charge : 5.500018 assigned positive charge : 422.6028 centred at (gu) : 90.20879 86.75649 85.43376 assigned negative charge : -417.1034 centred at (gu) : 90.52261 86.94926 84.68195 start vw surface at 0.1100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 161173 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32086 grid for indexing accessible points = 1.400000 m= 73006 mr = 105212 m= 23496 mr = 54179 m= 4421 mr = 16691 m= 444 mr = 2632 m= 18 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9000000 number of dielectric boundary points 83681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 21911 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) : 1.727764 object centre at (A) : 142.0520 -16.52450 75.43900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4960473E-02 0.3457243 midg,1,midg; midg,igrid,midg 0.1101040 0.1193944 1,midg,midg; igrid,midg,midg 0.2117677 6.4294755E-02 gauss-seidel spectral radius is 0.9992294 estimated iterations to convergence 284 setup time was (sec) 1.140000 now iterating at: 09:44:19 rms-change max change #iterations 9.413498 322.7789 at 10iterations 5.562928 171.0502 at 20iterations 3.244629 85.85271 at 30iterations 1.880019 48.20953 at 40iterations 1.084460 23.66951 at 50iterations 0.6225010 14.45379 at 60iterations 0.3570955 8.715012 at 70iterations 0.2036119 5.652552 at 80iterations 0.1162461 2.555763 at 90iterations 6.6447735E-02 1.459742 at 100iterations 3.7758980E-02 0.8324242 at 110iterations 2.1523036E-02 0.5120182 at 120iterations 1.2200053E-02 0.2544121 at 130iterations 6.9373269E-03 0.1439905 at 140iterations 3.9439225E-03 7.7735901E-02 at 150iterations 2.2420103E-03 4.5550585E-02 at 160iterations 1.2714656E-03 2.5479317E-02 at 170iterations 7.2140823E-04 1.4115810E-02 at 180iterations finished qdiffx linear iterations at : 09:44:30 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 7.2140823E-04 1.4115810E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 09:44:31 12.864u 0.228s 0:13.44 97.3% 0+0k 0+0io 0pf+0w