Sat Oct 8 14:09:01 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 Sat Oct 8 2011 at 14:09:01 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 !!! WARNING: NAP 500 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6368287 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): -12.09700 43.49200 ymin,ymax (A): -22.26100 22.66900 zmin,zma (A): -8.348001 47.55400 x,y,z range (A): 55.58900 44.93000 55.90200 scale (grids/A): 0.6368287 object centre (A): 15.69750 0.2039995 19.60300 number of atom coordinates read : 3038 total number of charged atoms : 2891 net assigned charge : 7.1674585E-06 assigned positive charge : 454.8036 centred at (gu) : 88.76378 89.54214 91.96391 assigned negative charge : -454.8043 centred at (gu) : 88.75862 89.44726 91.86633 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8174 nv = 96 ne = 84 npr = 63752 no. pairs analyzed = 63752 no. exposed pairs = 3436 no. arc points = 23984 no. surface atoms = 1175 nbur = 1863 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 4811 m= 0 mr = 45 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2262 ## 194 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9902 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.1513134E-09 1.8310121E-08 midg,1,midg; midg,igrid,midg -1.3418441E-08 1.0417737E-08 1,midg,midg; igrid,midg,midg -1.0900669E-09 3.4827838E-10 gauss-seidel spectral radius is 0.9872571 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 14:09:02 rms-change max change #iterations 0.1564586 24.00433 at 10iterations 1.5665574E-02 2.282539 at 20iterations 1.6176647E-03 0.2044830 at 30iterations 1.9680589E-04 2.6191711E-02 at 40iterations 3.0582047E-05 4.1770935E-03 at 50iterations finished qdiffx linear iterations at : 14:09:04 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 3.0582047E-05 4.1770935E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 14:09:04 3.133u 0.146s 0:03.56 91.8% 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 Sat Oct 8 2011 at 14:09:05 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 !!! WARNING: NAP 500 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.910486 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): -12.09700 43.49200 ymin,ymax (A): -22.26100 22.66900 zmin,zma (A): -8.348001 47.55400 x,y,z range (A): 55.58900 44.93000 55.90200 scale (grids/A): 1.910486 object centre (A): 15.69750 0.2039995 19.60300 number of atom coordinates read : 3038 total number of charged atoms : 2891 net assigned charge : 7.1674585E-06 assigned positive charge : 454.8036 centred at (gu) : 86.29102 88.62569 95.89106 assigned negative charge : -454.8043 centred at (gu) : 86.27578 88.34122 95.59852 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 88833 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23984 grid for indexing accessible points = 1.400000 m= 32017 mr = 64344 m= 4699 mr = 24131 m= 263 mr = 2710 m= 2 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 34544 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 22734 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) : 0.6368287 object centre at (A) : 15.69750 0.2039995 19.60300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3801025E-02 2.8068585E-02 midg,1,midg; midg,igrid,midg -1.2092107E-03 1.9624764E-02 1,midg,midg; igrid,midg,midg -3.0076453E-02 2.1848367E-03 gauss-seidel spectral radius is 0.9986773 estimated iterations to convergence 218 setup time was (sec) 0.8400000 now iterating at: 14:09:06 rms-change max change #iterations 4.699298 181.3708 at 10iterations 2.238241 67.62275 at 20iterations 1.059832 30.65381 at 30iterations 0.5028411 15.23894 at 40iterations 0.2386172 7.405270 at 50iterations 0.1136726 3.441624 at 60iterations 5.3968672E-02 1.608588 at 70iterations 2.5505789E-02 0.8365818 at 80iterations 1.2172827E-02 0.3878155 at 90iterations 5.7898229E-03 0.1563873 at 100iterations 2.7577386E-03 8.0310822E-02 at 110iterations 1.3110295E-03 3.9566040E-02 at 120iterations finished qdiffx linear iterations at : 14:09:12 total time elapsed so far: 6.900000 # loops : 120 mean,max change (kT/e) : 1.3110295E-03 3.9566040E-02 energy calculations done at 6.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 14:09:12 7.072u 0.195s 0:07.55 96.1% 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 Sat Oct 8 2011 at 14:09:12 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 !!! WARNING: NAP 500 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: 2.865729 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): -12.09700 43.49200 ymin,ymax (A): -22.26100 22.66900 zmin,zma (A): -8.348001 47.55400 x,y,z range (A): 55.58900 44.93000 55.90200 scale (grids/A): 2.865729 object centre (A): 15.69750 0.2039995 19.60300 number of atom coordinates read : 3038 total number of charged atoms : 2891 net assigned charge : 7.1674585E-06 assigned positive charge : 454.8036 centred at (gu) : 84.43637 87.93852 98.83627 assigned negative charge : -454.8043 centred at (gu) : 84.41363 87.51189 98.39777 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 205918 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23984 grid for indexing accessible points = 1.400000 m= 105165 mr = 155668 m= 36790 mr = 87513 m= 8245 mr = 29598 m= 1144 mr = 5844 m= 64 mr = 711 m= 0 mr = 22 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.510000 number of dielectric boundary points 77970 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 23127 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) : 1.910486 object centre at (A) : 15.69750 0.2039995 19.60300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1223257 0.4147668 midg,1,midg; midg,igrid,midg 6.3615600E-03 0.2126525 1,midg,midg; igrid,midg,midg -0.5356166 6.3413016E-02 gauss-seidel spectral radius is 0.9992739 estimated iterations to convergence 293 setup time was (sec) 1.800000 now iterating at: 14:09:14 rms-change max change #iterations 10.91527 394.3843 at 10iterations 6.418598 133.8562 at 20iterations 3.749522 74.25151 at 30iterations 2.189401 38.23796 at 40iterations 1.271267 24.96361 at 50iterations 0.7397185 13.00018 at 60iterations 0.4282446 7.235312 at 70iterations 0.2486925 4.235774 at 80iterations 0.1442258 2.566570 at 90iterations 8.3537303E-02 1.365527 at 100iterations 4.8424352E-02 0.8318348 at 110iterations 2.8023539E-02 0.4600873 at 120iterations 1.6243897E-02 0.2793579 at 130iterations 9.4272355E-03 0.1596813 at 140iterations 5.4790890E-03 8.8252068E-02 at 150iterations 3.2000018E-03 5.2904129E-02 at 160iterations 1.8834398E-03 3.3958435E-02 at 170iterations 1.1154718E-03 1.9340515E-02 at 180iterations finished qdiffx linear iterations at : 14:09:24 total time elapsed so far: 11.45000 # loops : 180 mean,max change (kT/e) : 1.1154718E-03 1.9340515E-02 energy calculations done at 11.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.62000 DelPhi exited at 14:09:24 11.624u 0.221s 0:12.12 97.6% 0+0k 0+0io 0pf+0w