Sun Oct 9 10:35:40 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 Sun Oct 9 2011 at 10:35:41 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2644 !!! WARNING: HIR 214 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6325403 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): -13.81500 42.46600 ymin,ymax (A): 17.11400 71.28600 zmin,zma (A): -3.520000 47.48100 x,y,z range (A): 56.28100 54.17200 51.00100 scale (grids/A): 0.6325403 object centre (A): 14.32550 44.20000 21.98050 number of atom coordinates read : 2644 total number of charged atoms : 2500 net assigned charge : -3.485983 assigned positive charge : 383.9345 centred at (gu) : 91.01071 90.31169 91.73884 assigned negative charge : -387.4217 centred at (gu) : 90.98619 90.25985 91.79971 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7458 nv = 96 ne = 84 npr = 52601 no. pairs analyzed = 52601 no. exposed pairs = 3526 no. arc points = 24900 no. surface atoms = 1191 nbur = 1453 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 413 mr = 3949 m= 4 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.2000000 number of dielectric boundary points 3889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2299 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8658 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1127548E-09 -1.4290338E-08 midg,1,midg; midg,igrid,midg -8.3405807E-09 9.4504693E-10 1,midg,midg; igrid,midg,midg -5.1010614E-09 -2.0534310E-09 gauss-seidel spectral radius is 0.9870710 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 10:35:41 rms-change max change #iterations 0.1373913 23.69164 at 10iterations 1.3393337E-02 2.248276 at 20iterations 1.2968259E-03 0.2375908 at 30iterations 1.6147975E-04 2.3332596E-02 at 40iterations 5.6321969E-05 8.7511539E-03 at 50iterations finished qdiffx linear iterations at : 10:35:44 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 5.6321969E-05 8.7511539E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 10:35:44 3.428u 0.166s 0:03.88 92.2% 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 Sun Oct 9 2011 at 10:35:44 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2644 !!! WARNING: HIR 214 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.897621 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): -13.81500 42.46600 ymin,ymax (A): 17.11400 71.28600 zmin,zma (A): -3.520000 47.48100 x,y,z range (A): 56.28100 54.17200 51.00100 scale (grids/A): 1.897621 object centre (A): 14.32550 44.20000 21.98050 number of atom coordinates read : 2644 total number of charged atoms : 2500 net assigned charge : -3.485983 assigned positive charge : 383.9345 centred at (gu) : 93.03147 90.93444 95.21600 assigned negative charge : -387.4217 centred at (gu) : 92.95852 90.77952 95.39890 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80074 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24900 grid for indexing accessible points = 1.400000 m= 28149 mr = 54396 m= 4631 mr = 20025 m= 294 mr = 2761 m= 3 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 35871 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 19694 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) : 0.6325403 object centre at (A) : 14.32550 44.20000 21.98050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4663758E-02 6.9326255E-03 midg,1,midg; midg,igrid,midg -3.8197145E-02 -1.5124089E-02 1,midg,midg; igrid,midg,midg 7.4124741E-03 2.3992050E-02 gauss-seidel spectral radius is 0.9986523 estimated iterations to convergence 216 setup time was (sec) 0.6200000 now iterating at: 10:35:45 rms-change max change #iterations 4.233367 196.2406 at 10iterations 1.980534 67.12147 at 20iterations 0.9327542 28.86715 at 30iterations 0.4371222 14.05806 at 40iterations 0.2057904 6.323935 at 50iterations 9.6658453E-02 3.182755 at 60iterations 4.5438427E-02 1.411621 at 70iterations 2.1460850E-02 0.6143870 at 80iterations 1.0073714E-02 0.3837948 at 90iterations 4.7513465E-03 0.1476383 at 100iterations 2.2442632E-03 7.0692182E-02 at 110iterations 1.0564125E-03 3.9632797E-02 at 120iterations finished qdiffx linear iterations at : 10:35:52 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 1.0564125E-03 3.9632797E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 10:35:53 7.944u 0.205s 0:08.43 96.5% 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 Sun Oct 9 2011 at 10:35:53 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2644 !!! WARNING: HIR 214 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.846431 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): -13.81500 42.46600 ymin,ymax (A): 17.11400 71.28600 zmin,zma (A): -3.520000 47.48100 x,y,z range (A): 56.28100 54.17200 51.00100 scale (grids/A): 2.846431 object centre (A): 14.32550 44.20000 21.98050 number of atom coordinates read : 2644 total number of charged atoms : 2500 net assigned charge : -3.485983 assigned positive charge : 383.9345 centred at (gu) : 94.54697 91.40150 97.82375 assigned negative charge : -387.4217 centred at (gu) : 94.43777 91.16922 98.09833 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 185306 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24900 grid for indexing accessible points = 1.400000 m= 91045 mr = 132568 m= 32894 mr = 72555 m= 8294 mr = 25793 m= 1244 mr = 6129 m= 56 mr = 766 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.000000 number of dielectric boundary points 81023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 19995 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) : 1.897621 object centre at (A) : 14.32550 44.20000 21.98050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1426083 0.2166070 midg,1,midg; midg,igrid,midg -0.4104078 -0.1222385 1,midg,midg; igrid,midg,midg 0.1096251 0.4015627 gauss-seidel spectral radius is 0.9992760 estimated iterations to convergence 293 setup time was (sec) 1.230000 now iterating at: 10:35:54 rms-change max change #iterations 10.09780 335.1034 at 10iterations 6.006893 123.9954 at 20iterations 3.551597 70.91537 at 30iterations 2.088184 39.86469 at 40iterations 1.222324 26.54240 at 50iterations 0.7146367 12.50095 at 60iterations 0.4169431 7.028396 at 70iterations 0.2429579 4.419623 at 80iterations 0.1412905 2.585345 at 90iterations 8.1752010E-02 1.497961 at 100iterations 4.7551259E-02 0.8591461 at 110iterations 2.7588863E-02 0.5306530 at 120iterations 1.6027927E-02 0.2937012 at 130iterations 9.2709260E-03 0.1567855 at 140iterations 5.3845742E-03 0.1113777 at 150iterations 3.1116058E-03 5.9731483E-02 at 160iterations 1.8016307E-03 3.2669485E-02 at 170iterations 1.0449404E-03 1.8659651E-02 at 180iterations finished qdiffx linear iterations at : 10:36:06 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 1.0449404E-03 1.8659651E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.85000 DelPhi exited at 10:36:06 12.856u 0.223s 0:13.39 97.6% 0+0k 0+0io 0pf+0w