Tue Oct 11 06:28:29 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 06:28:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2132 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: 0.6990948 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): 2.687000 43.41300 ymin,ymax (A): 6.847000 51.04400 zmin,zma (A): 2.151000 53.07400 x,y,z range (A): 40.72600 44.19700 50.92300 scale (grids/A): 0.6990948 object centre (A): 23.05000 28.94550 27.61250 number of atom coordinates read : 2132 total number of charged atoms : 2004 net assigned charge : 6.500009 assigned positive charge : 326.6799 centred at (gu) : 89.23409 89.88184 88.88248 assigned negative charge : -320.1801 centred at (gu) : 89.13504 89.96461 88.83612 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6820 nv = 96 ne = 84 npr = 42583 no. pairs analyzed = 42583 no. exposed pairs = 2911 no. arc points = 19209 no. surface atoms = 979 nbur = 1153 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 509 mr = 3614 m= 5 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1758 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7718 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1760504E-08 5.2273482E-08 midg,1,midg; midg,igrid,midg 8.1747856E-08 1.0247071E-08 1,midg,midg; igrid,midg,midg 3.5721410E-09 7.4592307E-08 gauss-seidel spectral radius is 0.9893392 estimated iterations to convergence 79 setup time was (sec) 0.4700000 now iterating at: 06:28:30 rms-change max change #iterations 0.1939382 27.48565 at 10iterations 2.3416897E-02 3.913833 at 20iterations 2.9105137E-03 0.4925766 at 30iterations 5.5651780E-04 6.8507195E-02 at 40iterations 1.8578992E-04 2.1568298E-02 at 50iterations finished qdiffx linear iterations at : 06:28:32 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 1.8578992E-04 2.1568298E-02 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 06:28:33 3.075u 0.144s 0:03.95 81.2% 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 Tue Oct 11 2011 at 06:28:33 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 = 2132 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.097284 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): 2.687000 43.41300 ymin,ymax (A): 6.847000 51.04400 zmin,zma (A): 2.151000 53.07400 x,y,z range (A): 40.72600 44.19700 50.92300 scale (grids/A): 2.097284 object centre (A): 23.05000 28.94550 27.61250 number of atom coordinates read : 2132 total number of charged atoms : 2004 net assigned charge : 6.500009 assigned positive charge : 326.6799 centred at (gu) : 87.70216 89.64549 86.64726 assigned negative charge : -320.1801 centred at (gu) : 87.40530 89.89387 86.50836 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 70735 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19209 grid for indexing accessible points = 1.400000 m= 28664 mr = 47883 m= 5945 mr = 20619 m= 585 mr = 3627 m= 16 mr = 232 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 33584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15906 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) : 0.6990948 object centre at (A) : 23.05000 28.94550 27.61250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2252783E-02 1.2074969E-02 midg,1,midg; midg,igrid,midg 2.6804864E-02 1.7178543E-02 1,midg,midg; igrid,midg,midg 3.7239301E-03 4.0428545E-02 gauss-seidel spectral radius is 0.9988138 estimated iterations to convergence 230 setup time was (sec) 0.8700000 now iterating at: 06:28:34 rms-change max change #iterations 4.573461 182.2024 at 10iterations 2.255575 74.59010 at 20iterations 1.106449 35.56595 at 30iterations 0.5460877 17.46888 at 40iterations 0.2697579 8.055262 at 50iterations 0.1332373 3.955002 at 60iterations 6.5666080E-02 2.010417 at 70iterations 3.2405917E-02 1.094614 at 80iterations 1.6120929E-02 0.4764538 at 90iterations 8.0027180E-03 0.2529113 at 100iterations 4.0407674E-03 0.1348572 at 110iterations 2.0789613E-03 7.0251465E-02 at 120iterations finished qdiffx linear iterations at : 06:28:40 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 2.0789613E-03 7.0251465E-02 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.110000 DelPhi exited at 06:28:41 7.111u 0.158s 0:07.81 92.9% 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 06:28:41 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 = 2132 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 3.145926 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): 2.687000 43.41300 ymin,ymax (A): 6.847000 51.04400 zmin,zma (A): 2.151000 53.07400 x,y,z range (A): 40.72600 44.19700 50.92300 scale (grids/A): 3.145926 object centre (A): 23.05000 28.94550 27.61250 number of atom coordinates read : 2132 total number of charged atoms : 2004 net assigned charge : 6.500009 assigned positive charge : 326.6799 centred at (gu) : 86.55319 89.46817 84.97091 assigned negative charge : -320.1801 centred at (gu) : 86.10796 89.84083 84.76258 start vw surface at 0.1500000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 162916 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19209 grid for indexing accessible points = 1.400000 m= 87484 mr = 116392 m= 36879 mr = 70014 m= 11254 mr = 29223 m= 2274 mr = 8110 m= 303 mr = 1438 m= 11 mr = 162 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.700000 number of dielectric boundary points 75778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 16032 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) : 2.097284 object centre at (A) : 23.05000 28.94550 27.61250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4107840 -5.7300027E-02 midg,1,midg; midg,igrid,midg 0.1830628 0.2158948 1,midg,midg; igrid,midg,midg 1.9840501E-02 0.4116562 gauss-seidel spectral radius is 0.9993042 estimated iterations to convergence 299 setup time was (sec) 1.980000 now iterating at: 06:28:43 rms-change max change #iterations 10.42370 316.4654 at 10iterations 6.264671 136.3416 at 20iterations 3.748509 91.77291 at 30iterations 2.226910 46.70514 at 40iterations 1.325845 26.19921 at 50iterations 0.7840850 17.03035 at 60iterations 0.4644959 8.169279 at 70iterations 0.2739914 5.366776 at 80iterations 0.1613904 2.818722 at 90iterations 9.5041998E-02 1.547304 at 100iterations 5.5989828E-02 1.093829 at 110iterations 3.2918915E-02 0.6449471 at 120iterations 1.9449404E-02 0.3540058 at 130iterations 1.1519417E-02 0.2396545 at 140iterations 6.8695173E-03 0.1256790 at 150iterations 4.1840118E-03 7.8414917E-02 at 160iterations 2.6306023E-03 5.2209854E-02 at 170iterations 1.7459457E-03 3.1468391E-02 at 180iterations finished qdiffx linear iterations at : 06:28:53 total time elapsed so far: 11.89000 # loops : 180 mean,max change (kT/e) : 1.7459457E-03 3.1468391E-02 energy calculations done at 11.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.06000 DelPhi exited at 06:28:54 12.061u 0.192s 0:12.80 95.7% 0+0k 0+0io 0pf+0w