Tue Oct 11 02:44:24 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 02:44:24 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: FMN 398 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: 0.6650228 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): -22.19100 24.84400 ymin,ymax (A): 10.57200 64.10400 zmin,zma (A): -17.38900 30.13300 x,y,z range (A): 47.03500 53.53200 47.52200 scale (grids/A): 0.6650228 object centre (A): 1.326500 37.33800 6.372001 number of atom coordinates read : 2756 total number of charged atoms : 2622 net assigned charge : 5.000025 assigned positive charge : 425.1833 centred at (gu) : 89.20793 89.64916 90.52193 assigned negative charge : -420.1843 centred at (gu) : 89.39940 89.43944 90.56409 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8268 nv = 96 ne = 84 npr = 56349 no. pairs analyzed = 56349 no. exposed pairs = 3453 no. arc points = 23364 no. surface atoms = 1159 nbur = 1597 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 453 mr = 4698 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.3800000 number of dielectric boundary points 3965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2193 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9607 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2214506E-08 4.5804569E-09 midg,1,midg; midg,igrid,midg -4.0648132E-08 5.9877387E-08 1,midg,midg; igrid,midg,midg 7.0972604E-08 -2.7856053E-08 gauss-seidel spectral radius is 0.9882934 estimated iterations to convergence 75 setup time was (sec) 0.6400000 now iterating at: 02:44:25 rms-change max change #iterations 0.1814363 24.36636 at 10iterations 2.0461436E-02 3.090351 at 20iterations 3.1996351E-03 0.5283051 at 30iterations 9.6602831E-04 0.2020798 at 40iterations 3.6874335E-04 7.9010010E-02 at 50iterations finished qdiffx linear iterations at : 02:44:28 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 3.6874335E-04 7.9010010E-02 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 02:44:29 4.177u 0.271s 0:04.80 92.5% 0+0k 0+0io 4pf+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 02:44:29 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: FMN 398 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: 1.995068 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): -22.19100 24.84400 ymin,ymax (A): 10.57200 64.10400 zmin,zma (A): -17.38900 30.13300 x,y,z range (A): 47.03500 53.53200 47.52200 scale (grids/A): 1.995068 object centre (A): 1.326500 37.33800 6.372001 number of atom coordinates read : 2756 total number of charged atoms : 2622 net assigned charge : 5.000025 assigned positive charge : 425.1833 centred at (gu) : 87.62330 88.94672 91.56514 assigned negative charge : -420.1843 centred at (gu) : 88.19785 88.31821 91.69193 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 88436 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23364 grid for indexing accessible points = 1.400000 m= 33758 mr = 62455 m= 5955 mr = 25517 m= 413 mr = 3932 m= 6 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 1263 time to turn everything in is 0.7900000 number of dielectric boundary points 36503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 20717 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) : 0.6650228 object centre at (A) : 1.326500 37.33800 6.372001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4608023E-02 -2.1987228E-02 midg,1,midg; midg,igrid,midg -4.1914191E-02 6.8757340E-02 1,midg,midg; igrid,midg,midg 7.0170589E-02 -1.7519211E-02 gauss-seidel spectral radius is 0.9987686 estimated iterations to convergence 226 setup time was (sec) 1.090000 now iterating at: 02:44:31 rms-change max change #iterations 4.905668 217.3527 at 10iterations 2.388260 80.20910 at 20iterations 1.160710 38.09880 at 30iterations 0.5662987 18.16801 at 40iterations 0.2766199 8.467804 at 50iterations 0.1345216 3.834846 at 60iterations 6.5623626E-02 1.865509 at 70iterations 3.2216046E-02 1.094779 at 80iterations 1.6033454E-02 0.4750595 at 90iterations 8.1315553E-03 0.2514839 at 100iterations 4.2961291E-03 0.1732941 at 110iterations 2.4160885E-03 8.5689545E-02 at 120iterations finished qdiffx linear iterations at : 02:44:39 total time elapsed so far: 9.720000 # loops : 120 mean,max change (kT/e) : 2.4160885E-03 8.5689545E-02 energy calculations done at 9.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.900000 DelPhi exited at 02:44:40 9.904u 0.323s 0:10.67 95.7% 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 02:44:40 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: FMN 398 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: 2.992603 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): -22.19100 24.84400 ymin,ymax (A): 10.57200 64.10400 zmin,zma (A): -17.38900 30.13300 x,y,z range (A): 47.03500 53.53200 47.52200 scale (grids/A): 2.992603 object centre (A): 1.326500 37.33800 6.372001 number of atom coordinates read : 2756 total number of charged atoms : 2622 net assigned charge : 5.000025 assigned positive charge : 425.1833 centred at (gu) : 86.43478 88.41977 92.34760 assigned negative charge : -420.1843 centred at (gu) : 87.29680 87.47713 92.53773 start vw surface at 0.1600000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 204010 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23364 grid for indexing accessible points = 1.400000 m= 107619 mr = 150726 m= 41545 mr = 89183 m= 10852 mr = 33957 m= 1870 mr = 8462 m= 141 mr = 1323 m= 1 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 4531 time to turn everything in is 2.070000 number of dielectric boundary points 82321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 20976 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) : 1.995068 object centre at (A) : 1.326500 37.33800 6.372001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2032793 -0.2538521 midg,1,midg; midg,igrid,midg -0.5686086 0.9614056 1,midg,midg; igrid,midg,midg 0.6757806 -0.1828528 gauss-seidel spectral radius is 0.9992934 estimated iterations to convergence 297 setup time was (sec) 2.420000 now iterating at: 02:44:43 rms-change max change #iterations 11.19249 472.5103 at 10iterations 6.621384 136.5033 at 20iterations 3.908026 82.67560 at 30iterations 2.299212 51.13837 at 40iterations 1.350649 28.76149 at 50iterations 0.7914522 14.43927 at 60iterations 0.4623621 8.376869 at 70iterations 0.2713122 4.543890 at 80iterations 0.1584994 2.734024 at 90iterations 9.2586286E-02 1.659367 at 100iterations 5.4182615E-02 0.9621925 at 110iterations 3.1743988E-02 0.6215744 at 120iterations 1.8656563E-02 0.3324699 at 130iterations 1.1004739E-02 0.1924210 at 140iterations 6.6424026E-03 0.1226730 at 150iterations 4.1036406E-03 9.2025757E-02 at 160iterations 2.6605430E-03 6.1508179E-02 at 170iterations 1.8335982E-03 4.2999268E-02 at 180iterations finished qdiffx linear iterations at : 02:44:57 total time elapsed so far: 16.91000 # loops : 180 mean,max change (kT/e) : 1.8335982E-03 4.2999268E-02 energy calculations done at 16.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.10000 DelPhi exited at 02:44:58 17.099u 0.322s 0:17.80 97.8% 0+0k 0+0io 0pf+0w