Sun Oct 9 14:52:02 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 Sun Oct 9 2011 at 14:52:02 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 = 1252 !!! WARNING: GLU 107 has a net charge of -2.0000 !!! WARNING: GLU 214 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7103803 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): 42.86000 92.97400 ymin,ymax (A): -27.86200 14.27300 zmin,zma (A): -31.61300 16.53500 x,y,z range (A): 50.11400 42.13500 48.14800 scale (grids/A): 0.7103803 object centre (A): 67.91700 -6.794500 -7.539000 number of atom coordinates read : 1252 total number of charged atoms : 1122 net assigned charge : 1.500005 assigned positive charge : 179.4063 centred at (gu) : 89.22391 89.79609 91.98806 assigned negative charge : -177.9061 centred at (gu) : 89.25076 89.64568 91.89796 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4574 nv = 96 ne = 84 npr = 24460 no. pairs analyzed = 24460 no. exposed pairs = 1718 no. arc points = 12911 no. surface atoms = 573 nbur = 679 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 254 mr = 2303 m= 0 mr = 37 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 75 time to turn everything in is 0.1300000 number of dielectric boundary points 2488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1040 ## 100 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 4545 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.4296357E-09 5.8850567E-08 midg,1,midg; midg,igrid,midg -3.4174793E-08 5.5155059E-08 1,midg,midg; igrid,midg,midg 2.4395947E-08 4.3218988E-09 gauss-seidel spectral radius is 0.9896026 estimated iterations to convergence 80 setup time was (sec) 0.3200000 now iterating at: 14:52:02 rms-change max change #iterations 0.1518361 31.31332 at 10iterations 1.8595312E-02 3.469398 at 20iterations 2.2437568E-03 0.3906708 at 30iterations 2.7218938E-04 4.7271729E-02 at 40iterations 3.2850687E-05 5.6021214E-03 at 50iterations finished qdiffx linear iterations at : 14:52:05 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 3.2850687E-05 5.6021214E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 14:52:06 3.347u 0.178s 0:03.79 92.6% 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 14:52:06 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 = 1252 !!! WARNING: GLU 107 has a net charge of -2.0000 !!! WARNING: GLU 214 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.131141 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): 42.86000 92.97400 ymin,ymax (A): -27.86200 14.27300 zmin,zma (A): -31.61300 16.53500 x,y,z range (A): 50.11400 42.13500 48.14800 scale (grids/A): 2.131141 object centre (A): 67.91700 -6.794500 -7.539000 number of atom coordinates read : 1252 total number of charged atoms : 1122 net assigned charge : 1.500005 assigned positive charge : 179.4063 centred at (gu) : 87.67213 89.38863 95.96429 assigned negative charge : -177.9061 centred at (gu) : 87.75253 88.93695 95.69411 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 47457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12911 grid for indexing accessible points = 1.400000 m= 17591 mr = 30439 m= 3018 mr = 12839 m= 211 mr = 1955 m= 4 mr = 101 m= 0 mr = 2 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 2110 time to turn everything in is 0.2500000 number of dielectric boundary points 22945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 51 iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8935 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) : 0.7103803 object centre at (A) : 67.91700 -6.794500 -7.539000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8059717E-03 8.8808760E-03 midg,1,midg; midg,igrid,midg 1.0595048E-03 1.9354353E-02 1,midg,midg; igrid,midg,midg 1.4059682E-02 1.5968477E-02 gauss-seidel spectral radius is 0.9987698 estimated iterations to convergence 226 setup time was (sec) 0.4800000 now iterating at: 14:52:06 rms-change max change #iterations 3.436648 174.1054 at 10iterations 1.653335 74.24579 at 20iterations 0.8007694 35.73330 at 30iterations 0.3891452 15.02811 at 40iterations 0.1887037 7.264175 at 50iterations 9.1157436E-02 3.248053 at 60iterations 4.4437613E-02 2.044922 at 70iterations 2.1421989E-02 0.8223114 at 80iterations 1.0472869E-02 0.3926563 at 90iterations 5.0415415E-03 0.2206702 at 100iterations 2.4617850E-03 9.6488953E-02 at 110iterations 1.1953813E-03 4.5196533E-02 at 120iterations finished qdiffx linear iterations at : 14:52:13 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.1953813E-03 4.5196533E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 14:52:14 7.684u 0.187s 0:08.15 96.4% 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 14:52:14 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 = 1252 !!! WARNING: GLU 107 has a net charge of -2.0000 !!! WARNING: GLU 214 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.196711 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): 42.86000 92.97400 ymin,ymax (A): -27.86200 14.27300 zmin,zma (A): -31.61300 16.53500 x,y,z range (A): 50.11400 42.13500 48.14800 scale (grids/A): 3.196711 object centre (A): 67.91700 -6.794500 -7.539000 number of atom coordinates read : 1252 total number of charged atoms : 1122 net assigned charge : 1.500005 assigned positive charge : 179.4063 centred at (gu) : 86.50828 89.08294 98.94643 assigned negative charge : -177.9061 centred at (gu) : 86.62882 88.40551 98.54115 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 109087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12911 grid for indexing accessible points = 1.400000 m= 54992 mr = 73577 m= 21528 mr = 44700 m= 5578 mr = 17319 m= 876 mr = 4227 m= 90 mr = 580 m= 5 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 7209 time to turn everything in is 0.7500000 number of dielectric boundary points 51700 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 8976 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) : 2.131141 object centre at (A) : 67.91700 -6.794500 -7.539000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9187743E-02 0.3167043 midg,1,midg; midg,igrid,midg 1.1306891E-02 0.1400836 1,midg,midg; igrid,midg,midg 0.1925087 0.2044886 gauss-seidel spectral radius is 0.9992886 estimated iterations to convergence 296 setup time was (sec) 0.9800000 now iterating at: 14:52:15 rms-change max change #iterations 7.853439 488.2225 at 10iterations 4.595176 133.5231 at 20iterations 2.696099 73.25368 at 30iterations 1.578743 40.91743 at 40iterations 0.9194019 21.01594 at 50iterations 0.5342374 11.53265 at 60iterations 0.3109583 6.883594 at 70iterations 0.1807469 3.647472 at 80iterations 0.1051603 2.266479 at 90iterations 6.1017055E-02 1.263288 at 100iterations 3.5436410E-02 0.7332230 at 110iterations 2.0533197E-02 0.4347334 at 120iterations 1.1939255E-02 0.2668724 at 130iterations 6.9040069E-03 0.1442645 at 140iterations 4.0067607E-03 8.4190965E-02 at 150iterations 2.3227809E-03 5.5622458E-02 at 160iterations 1.3473287E-03 2.9296875E-02 at 170iterations 7.8197784E-04 1.6272426E-02 at 180iterations finished qdiffx linear iterations at : 14:52:26 total time elapsed so far: 11.92000 # loops : 180 mean,max change (kT/e) : 7.8197784E-04 1.6272426E-02 energy calculations done at 11.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.05000 DelPhi exited at 14:52:26 12.056u 0.201s 0:12.53 97.7% 0+0k 0+0io 0pf+0w