Sun Oct 9 11:56:07 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 11:56:07 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2681 !!! WARNING: HIQ 202 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: 0.6634859 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): 51.83600 104.2770 ymin,ymax (A): 5.218000 55.91600 zmin,zma (A): 34.47900 88.13500 x,y,z range (A): 52.44100 50.69800 53.65600 scale (grids/A): 0.6634859 object centre (A): 78.05650 30.56700 61.30700 number of atom coordinates read : 2681 total number of charged atoms : 2540 net assigned charge : 0.5140090 assigned positive charge : 386.1542 centred at (gu) : 89.25437 90.05189 92.68508 assigned negative charge : -385.6418 centred at (gu) : 89.42947 90.13725 92.60302 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 8535 nv = 96 ne = 84 npr = 52637 no. pairs analyzed = 52637 no. exposed pairs = 3618 no. arc points = 26070 no. surface atoms = 1228 nbur = 1453 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 595 mr = 4533 m= 5 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 4502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2280 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9534 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.7024255E-09 3.1951142E-08 midg,1,midg; midg,igrid,midg 1.8477543E-08 -1.7919321E-08 1,midg,midg; igrid,midg,midg 4.3668834E-08 -3.1944463E-08 gauss-seidel spectral radius is 0.9882559 estimated iterations to convergence 75 setup time was (sec) 0.3800000 now iterating at: 11:56:07 rms-change max change #iterations 0.1759400 20.58835 at 10iterations 1.9220458E-02 2.461342 at 20iterations 2.3131862E-03 0.3209457 at 30iterations 4.5314332E-04 8.1243515E-02 at 40iterations 1.4009849E-04 2.7263641E-02 at 50iterations finished qdiffx linear iterations at : 11:56:10 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.4009849E-04 2.7263641E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 11:56:11 3.370u 0.180s 0:03.82 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 Sun Oct 9 2011 at 11:56:11 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2681 !!! WARNING: HIQ 202 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: 1.990458 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): 51.83600 104.2770 ymin,ymax (A): 5.218000 55.91600 zmin,zma (A): 34.47900 88.13500 x,y,z range (A): 52.44100 50.69800 53.65600 scale (grids/A): 1.990458 object centre (A): 78.05650 30.56700 61.30700 number of atom coordinates read : 2681 total number of charged atoms : 2540 net assigned charge : 0.5140090 assigned positive charge : 386.1542 centred at (gu) : 87.76241 90.15497 98.05437 assigned negative charge : -385.6418 centred at (gu) : 88.28841 90.41158 97.80880 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 90455 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26070 grid for indexing accessible points = 1.400000 m= 35376 mr = 61077 m= 7479 mr = 25962 m= 642 mr = 5020 m= 13 mr = 308 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 41598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 20103 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) : 0.6634859 object centre at (A) : 78.05650 30.56700 61.30700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1966183E-02 8.2068682E-02 midg,1,midg; midg,igrid,midg 1.7928438E-02 -1.3698008E-02 1,midg,midg; igrid,midg,midg 3.4469210E-02 -4.1266762E-02 gauss-seidel spectral radius is 0.9987823 estimated iterations to convergence 227 setup time was (sec) 0.6600000 now iterating at: 11:56:11 rms-change max change #iterations 4.696334 196.1775 at 10iterations 2.294824 77.64291 at 20iterations 1.119130 36.36806 at 30iterations 0.5456434 18.27385 at 40iterations 0.2664332 8.036251 at 50iterations 0.1305282 3.789635 at 60iterations 6.3645720E-02 2.007248 at 70iterations 3.1138245E-02 0.9405289 at 80iterations 1.5271326E-02 0.4336863 at 90iterations 7.4934950E-03 0.2200279 at 100iterations 3.6945587E-03 0.1143379 at 110iterations 1.8441783E-03 5.5153847E-02 at 120iterations finished qdiffx linear iterations at : 11:56:19 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 1.8441783E-03 5.5153847E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 11:56:19 7.972u 0.205s 0:08.45 96.6% 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 11:56:19 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2681 !!! WARNING: HIQ 202 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: 2.985687 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): 51.83600 104.2770 ymin,ymax (A): 5.218000 55.91600 zmin,zma (A): 34.47900 88.13500 x,y,z range (A): 52.44100 50.69800 53.65600 scale (grids/A): 2.985687 object centre (A): 78.05650 30.56700 61.30700 number of atom coordinates read : 2681 total number of charged atoms : 2540 net assigned charge : 0.5140090 assigned positive charge : 386.1542 centred at (gu) : 86.64346 90.23232 102.0816 assigned negative charge : -385.6418 centred at (gu) : 87.43255 90.61740 101.7132 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 208378 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26070 grid for indexing accessible points = 1.400000 m= 108663 mr = 148308 m= 45816 mr = 87803 m= 14332 mr = 37049 m= 2820 mr = 11059 m= 229 mr = 2070 m= 5 mr = 127 m= 0 mr = 3 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 93824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 20320 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) : 1.990458 object centre at (A) : 78.05650 30.56700 61.30700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7302385E-02 1.045799 midg,1,midg; midg,igrid,midg 0.1825545 -0.3897119 1,midg,midg; igrid,midg,midg 0.3613619 -0.3973185 gauss-seidel spectral radius is 0.9993189 estimated iterations to convergence 302 setup time was (sec) 1.420000 now iterating at: 11:56:21 rms-change max change #iterations 10.91654 460.7610 at 10iterations 6.589096 141.4327 at 20iterations 3.953779 79.63842 at 30iterations 2.362542 48.98758 at 40iterations 1.408695 24.61682 at 50iterations 0.8346722 16.54098 at 60iterations 0.4951178 9.629200 at 70iterations 0.2932033 5.413864 at 80iterations 0.1733539 3.033256 at 90iterations 0.1022778 1.862172 at 100iterations 6.0422480E-02 0.9784088 at 110iterations 3.5709869E-02 0.6229718 at 120iterations 2.1046899E-02 0.3620567 at 130iterations 1.2397330E-02 0.2124138 at 140iterations 7.3256968E-03 0.1271057 at 150iterations 4.3396521E-03 7.1743011E-02 at 160iterations 2.5808469E-03 4.1858673E-02 at 170iterations 1.5454395E-03 2.5709152E-02 at 180iterations finished qdiffx linear iterations at : 11:56:33 total time elapsed so far: 13.21000 # loops : 180 mean,max change (kT/e) : 1.5454395E-03 2.5709152E-02 energy calculations done at 13.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 11:56:33 13.331u 0.241s 0:13.90 97.6% 0+0k 0+0io 0pf+0w