Wed Dec 21 14:21:10 PST 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 Wed Dec 21 2011 at 14:21:11 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 0.6420893 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): -5.823000 34.78900 ymin,ymax (A): -3.567000 49.04100 zmin,zma (A): -24.38400 31.06000 x,y,z range (A): 40.61200 52.60800 55.44400 scale (grids/A): 0.6420893 object centre (A): 14.48300 22.73700 3.338000 number of atom coordinates read : 1965 total number of charged atoms : 1832 net assigned charge : 2.681005 assigned positive charge : 287.8141 centred at (gu) : 90.84508 92.42708 90.18990 assigned negative charge : -285.1333 centred at (gu) : 90.96684 92.58059 90.12635 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5636 nv = 96 ne = 84 npr = 39735 no. pairs analyzed = 39735 no. exposed pairs = 2476 no. arc points = 17405 no. surface atoms = 838 nbur = 1127 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 317 mr = 3165 m= 0 mr = 48 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.3000000 number of dielectric boundary points 2740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1691 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6519 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0959194E-09 1.0703952E-08 midg,1,midg; midg,igrid,midg 1.0877971E-08 -1.6348928E-08 1,midg,midg; igrid,midg,midg 1.2869233E-08 -7.8632780E-09 gauss-seidel spectral radius is 0.9873784 estimated iterations to convergence 73 setup time was (sec) 0.5700000 now iterating at: 14:21:11 rms-change max change #iterations 0.1244481 17.97128 at 10iterations 1.2523481E-02 1.693741 at 20iterations 1.2313795E-03 0.1849136 at 30iterations 1.2065205E-04 1.7322540E-02 at 40iterations 1.2129063E-05 1.8234253E-03 at 50iterations finished qdiffx linear iterations at : 14:21:15 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 1.2129063E-05 1.8234253E-03 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 14:21:15 4.092u 0.252s 0:04.89 88.7% 0+0k 0+0io 6pf+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 Wed Dec 21 2011 at 14:21:15 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 1.926268 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): -5.823000 34.78900 ymin,ymax (A): -3.567000 49.04100 zmin,zma (A): -24.38400 31.06000 x,y,z range (A): 40.61200 52.60800 55.44400 scale (grids/A): 1.926268 object centre (A): 14.48300 22.73700 3.338000 number of atom coordinates read : 1965 total number of charged atoms : 1832 net assigned charge : 2.681005 assigned positive charge : 287.8141 centred at (gu) : 92.53531 97.28136 90.56964 assigned negative charge : -285.1333 centred at (gu) : 92.90068 97.74190 90.37925 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 60130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17405 grid for indexing accessible points = 1.400000 m= 23043 mr = 41686 m= 3965 mr = 17737 m= 212 mr = 2655 m= 1 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 2574 time to turn everything in is 0.5600000 number of dielectric boundary points 25184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 14458 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) : 0.6420893 object centre at (A) : 14.48300 22.73700 3.338000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1309826E-02 1.1762275E-02 midg,1,midg; midg,igrid,midg 3.3419196E-02 -1.3326342E-02 1,midg,midg; igrid,midg,midg 7.9588667E-03 -5.3729471E-03 gauss-seidel spectral radius is 0.9985893 estimated iterations to convergence 211 setup time was (sec) 0.8800000 now iterating at: 14:21:17 rms-change max change #iterations 3.610089 187.5811 at 10iterations 1.667000 63.40749 at 20iterations 0.7740229 27.14138 at 30iterations 0.3583765 12.20516 at 40iterations 0.1645944 5.501696 at 50iterations 7.6263316E-02 2.562325 at 60iterations 3.5214107E-02 1.211723 at 70iterations 1.6284714E-02 0.5342350 at 80iterations 7.5266631E-03 0.2780519 at 90iterations 3.4948324E-03 0.1447821 at 100iterations 1.6127550E-03 5.7240725E-02 at 110iterations 7.4626453E-04 2.4341583E-02 at 120iterations finished qdiffx linear iterations at : 14:21:25 total time elapsed so far: 9.230000 # loops : 120 mean,max change (kT/e) : 7.4626453E-04 2.4341583E-02 energy calculations done at 9.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.410000 DelPhi exited at 14:21:27 9.411u 0.324s 0:11.90 81.7% 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 Wed Dec 21 2011 at 14:21:27 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 2.889402 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): -5.823000 34.78900 ymin,ymax (A): -3.567000 49.04100 zmin,zma (A): -24.38400 31.06000 x,y,z range (A): 40.61200 52.60800 55.44400 scale (grids/A): 2.889402 object centre (A): 14.48300 22.73700 3.338000 number of atom coordinates read : 1965 total number of charged atoms : 1832 net assigned charge : 2.681005 assigned positive charge : 287.8141 centred at (gu) : 93.80283 100.9222 90.85445 assigned negative charge : -285.1333 centred at (gu) : 94.35109 101.6129 90.56910 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 138795 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17405 grid for indexing accessible points = 1.400000 m= 72848 mr = 100532 m= 28569 mr = 60794 m= 7181 mr = 23887 m= 985 mr = 5638 m= 64 mr = 705 m= 0 mr = 33 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 8409 time to turn everything in is 1.420000 number of dielectric boundary points 56853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 14655 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) : 1.926268 object centre at (A) : 14.48300 22.73700 3.338000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9744081 1.0015871E-02 midg,1,midg; midg,igrid,midg 0.3555267 -0.1501510 1,midg,midg; igrid,midg,midg 4.7339238E-02 -3.4593176E-02 gauss-seidel spectral radius is 0.9992329 estimated iterations to convergence 285 setup time was (sec) 1.740000 now iterating at: 14:21:30 rms-change max change #iterations 8.544590 539.5656 at 10iterations 4.917310 150.0706 at 20iterations 2.799127 77.44401 at 30iterations 1.595416 41.43279 at 40iterations 0.9127664 21.04839 at 50iterations 0.5194508 10.93930 at 60iterations 0.2957684 6.003477 at 70iterations 0.1679408 3.762016 at 80iterations 9.5542729E-02 2.138977 at 90iterations 5.4357063E-02 1.126801 at 100iterations 3.0904610E-02 0.6417096 at 110iterations 1.7531533E-02 0.3616776 at 120iterations 9.9552739E-03 0.2082386 at 130iterations 5.6614201E-03 0.1159821 at 140iterations 3.2165411E-03 6.4889908E-02 at 150iterations 1.8241502E-03 3.6739588E-02 at 160iterations 1.0351685E-03 2.1183014E-02 at 170iterations 5.8810931E-04 1.1219501E-02 at 180iterations finished qdiffx linear iterations at : 14:21:43 total time elapsed so far: 15.00000 # loops : 180 mean,max change (kT/e) : 5.8810931E-04 1.1219501E-02 energy calculations done at 15.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.18000 DelPhi exited at 14:21:45 15.183u 0.298s 0:17.12 90.3% 0+0k 0+0io 0pf+0w