Tue Oct 11 06:28:25 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 06:28:25 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1986 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7325706 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): -19.89800 23.87200 ymin,ymax (A): -10.14500 28.66700 zmin,zma (A): -36.75400 11.84200 x,y,z range (A): 43.77000 38.81200 48.59600 scale (grids/A): 0.7325706 object centre (A): 1.987000 9.261000 -12.45600 number of atom coordinates read : 1986 total number of charged atoms : 1902 net assigned charge : 5.931007 assigned positive charge : 307.8951 centred at (gu) : 90.01431 89.00687 91.04769 assigned negative charge : -301.9642 centred at (gu) : 89.84351 89.02726 91.13414 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7455 nv = 96 ne = 84 npr = 38506 no. pairs analyzed = 38506 no. exposed pairs = 2512 no. arc points = 17129 no. surface atoms = 846 nbur = 1140 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 553 mr = 4294 m= 7 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1588 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8078 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3158706E-07 2.0625892E-08 midg,1,midg; midg,igrid,midg 1.2761613E-07 6.0931825E-08 1,midg,midg; igrid,midg,midg -5.2901047E-08 2.2804142E-07 gauss-seidel spectral radius is 0.9902746 estimated iterations to convergence 82 setup time was (sec) 0.4600000 now iterating at: 06:28:25 rms-change max change #iterations 0.2321218 39.74497 at 10iterations 3.0938847E-02 4.056519 at 20iterations 4.3850639E-03 0.5744038 at 30iterations 8.0444798E-04 9.6221447E-02 at 40iterations 2.1404041E-04 2.6905060E-02 at 50iterations finished qdiffx linear iterations at : 06:28:28 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 2.1404041E-04 2.6905060E-02 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 06:28:29 3.313u 0.210s 0:03.81 92.3% 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 06:28:29 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1986 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.197712 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): -19.89800 23.87200 ymin,ymax (A): -10.14500 28.66700 zmin,zma (A): -36.75400 11.84200 x,y,z range (A): 43.77000 38.81200 48.59600 scale (grids/A): 2.197712 object centre (A): 1.987000 9.261000 -12.45600 number of atom coordinates read : 1986 total number of charged atoms : 1902 net assigned charge : 5.931007 assigned positive charge : 307.8951 centred at (gu) : 90.04289 87.02077 93.14314 assigned negative charge : -301.9642 centred at (gu) : 89.53049 87.08205 93.40252 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 78753 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17129 grid for indexing accessible points = 1.400000 m= 33572 mr = 56246 m= 7135 mr = 25778 m= 749 mr = 4825 m= 22 mr = 392 m= 0 mr = 4 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 32986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15145 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) : 0.7325706 object centre at (A) : 1.987000 9.261000 -12.45600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8981993E-02 6.5325829E-03 midg,1,midg; midg,igrid,midg 3.9219823E-02 7.7868346E-03 1,midg,midg; igrid,midg,midg 2.0732328E-02 5.7510328E-02 gauss-seidel spectral radius is 0.9988937 estimated iterations to convergence 238 setup time was (sec) 0.8800000 now iterating at: 06:28:30 rms-change max change #iterations 4.838707 191.4815 at 10iterations 2.446615 88.26472 at 20iterations 1.239758 41.71500 at 30iterations 0.6307027 19.51556 at 40iterations 0.3167346 9.635572 at 50iterations 0.1613750 4.771980 at 60iterations 8.1660517E-02 2.389105 at 70iterations 4.1514847E-02 1.269081 at 80iterations 2.1126552E-02 0.6222878 at 90iterations 1.0809677E-02 0.3036652 at 100iterations 5.5621951E-03 0.1689863 at 110iterations 2.9105854E-03 8.5491180E-02 at 120iterations finished qdiffx linear iterations at : 06:28:36 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 2.9105854E-03 8.5491180E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 06:28:37 7.620u 0.230s 0:08.67 90.5% 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 06:28:37 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1986 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.296568 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): -19.89800 23.87200 ymin,ymax (A): -10.14500 28.66700 zmin,zma (A): -36.75400 11.84200 x,y,z range (A): 43.77000 38.81200 48.59600 scale (grids/A): 3.296568 object centre (A): 1.987000 9.261000 -12.45600 number of atom coordinates read : 1986 total number of charged atoms : 1902 net assigned charge : 5.931007 assigned positive charge : 307.8951 centred at (gu) : 90.06440 85.53117 94.71475 assigned negative charge : -301.9642 centred at (gu) : 89.29565 85.62305 95.10382 start vw surface at 0.1200000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 180830 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17129 grid for indexing accessible points = 1.400000 m= 102296 mr = 134536 m= 44191 mr = 85725 m= 13789 mr = 36664 m= 2974 mr = 10713 m= 399 mr = 2185 m= 23 mr = 283 m= 0 mr = 9 time to grow re-entrant surface = 0.9300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.850000 number of dielectric boundary points 74387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 15212 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) : 2.197712 object centre at (A) : 1.987000 9.261000 -12.45600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2416818 -5.6407163E-03 midg,1,midg; midg,igrid,midg 0.2958800 3.0511068E-02 1,midg,midg; igrid,midg,midg 0.3747105 0.4436695 gauss-seidel spectral radius is 0.9993119 estimated iterations to convergence 301 setup time was (sec) 2.160000 now iterating at: 06:28:40 rms-change max change #iterations 10.63172 277.3936 at 10iterations 6.344253 136.8320 at 20iterations 3.775090 88.48543 at 30iterations 2.249065 40.74946 at 40iterations 1.331869 26.92514 at 50iterations 0.7877214 15.44431 at 60iterations 0.4659257 8.674936 at 70iterations 0.2753544 4.907867 at 80iterations 0.1623246 2.718662 at 90iterations 9.6059017E-02 1.644512 at 100iterations 5.7001643E-02 0.9550314 at 110iterations 3.3872060E-02 0.5850220 at 120iterations 2.0321211E-02 0.3943481 at 130iterations 1.2422878E-02 0.2208176 at 140iterations 7.8367814E-03 0.1461949 at 150iterations 5.1710932E-03 9.5069885E-02 at 160iterations 3.6121751E-03 6.3331604E-02 at 170iterations 2.6841499E-03 4.6375275E-02 at 180iterations finished qdiffx linear iterations at : 06:28:50 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 2.6841499E-03 4.6375275E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.64000 DelPhi exited at 06:28:51 12.642u 0.254s 0:13.29 96.9% 0+0k 0+0io 0pf+0w