Sat Oct 8 11:37:39 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 11:37:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3232 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: 0.6160662 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): 4.173000 61.67600 ymin,ymax (A): -8.339000 38.83400 zmin,zma (A): -19.50100 38.28500 x,y,z range (A): 57.50300 47.17300 57.78600 scale (grids/A): 0.6160662 object centre (A): 32.92450 15.24750 9.392000 number of atom coordinates read : 3232 total number of charged atoms : 3086 net assigned charge : -7.999964 assigned positive charge : 471.0155 centred at (gu) : 89.11616 90.36129 91.12959 assigned negative charge : -479.0168 centred at (gu) : 88.99036 90.43133 91.23302 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8235 nv = 96 ne = 84 npr = 67729 no. pairs analyzed = 67729 no. exposed pairs = 3928 no. arc points = 26656 no. surface atoms = 1333 nbur = 1899 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 4710 m= 7 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 72 time to turn everything in is 0.2500000 number of dielectric boundary points 3933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2595 ## 194 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 10166 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4810994E-09 -1.6853889E-08 midg,1,midg; midg,igrid,midg -3.9694481E-10 -1.1504492E-08 1,midg,midg; igrid,midg,midg -1.7999394E-08 2.8815590E-09 gauss-seidel spectral radius is 0.9864105 estimated iterations to convergence 70 setup time was (sec) 0.4600000 now iterating at: 11:37:41 rms-change max change #iterations 0.1370999 19.05796 at 10iterations 1.2569244E-02 1.582943 at 20iterations 1.3958887E-03 0.1939240 at 30iterations 3.2578170E-04 5.1841736E-02 at 40iterations 1.2039261E-04 1.7965317E-02 at 50iterations finished qdiffx linear iterations at : 11:37:45 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 1.2039261E-04 1.7965317E-02 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.900000 DelPhi exited at 11:37:45 3.899u 0.237s 0:04.50 91.5% 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 Sat Oct 8 2011 at 11:37:45 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 = 3232 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: 1.848199 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): 4.173000 61.67600 ymin,ymax (A): -8.339000 38.83400 zmin,zma (A): -19.50100 38.28500 x,y,z range (A): 57.50300 47.17300 57.78600 scale (grids/A): 1.848199 object centre (A): 32.92450 15.24750 9.392000 number of atom coordinates read : 3232 total number of charged atoms : 3086 net assigned charge : -7.999964 assigned positive charge : 471.0155 centred at (gu) : 87.34749 91.08302 93.38798 assigned negative charge : -479.0168 centred at (gu) : 86.97037 91.29352 93.69843 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 89761 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26656 grid for indexing accessible points = 1.400000 m= 32587 mr = 64207 m= 5090 mr = 24028 m= 289 mr = 3159 m= 6 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 3197 time to turn everything in is 0.4600000 number of dielectric boundary points 36266 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 24250 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) : 0.6160662 object centre at (A) : 32.92450 15.24750 9.392000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4083861E-02 -4.2209506E-02 midg,1,midg; midg,igrid,midg -2.4776546E-02 -3.0306982E-02 1,midg,midg; igrid,midg,midg -2.2803401E-03 5.0193485E-02 gauss-seidel spectral radius is 0.9986123 estimated iterations to convergence 213 setup time was (sec) 0.7100000 now iterating at: 11:37:47 rms-change max change #iterations 4.452131 153.2837 at 10iterations 2.070003 65.38408 at 20iterations 0.9645965 31.40999 at 30iterations 0.4490363 13.57299 at 40iterations 0.2099509 5.825417 at 50iterations 9.7918928E-02 2.778404 at 60iterations 4.5762345E-02 1.372925 at 70iterations 2.1347862E-02 0.6243591 at 80iterations 1.0039012E-02 0.3005562 at 90iterations 4.7479155E-03 0.1364279 at 100iterations 2.2850211E-03 7.4557781E-02 at 110iterations 1.1456399E-03 3.5503387E-02 at 120iterations finished qdiffx linear iterations at : 11:37:58 total time elapsed so far: 8.990000 # loops : 120 mean,max change (kT/e) : 1.1456399E-03 3.5503387E-02 energy calculations done at 8.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.120000 DelPhi exited at 11:37:58 9.125u 0.281s 0:13.02 72.1% 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 11:37:58 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 = 3232 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: 2.772298 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): 4.173000 61.67600 ymin,ymax (A): -8.339000 38.83400 zmin,zma (A): -19.50100 38.28500 x,y,z range (A): 57.50300 47.17300 57.78600 scale (grids/A): 2.772298 object centre (A): 32.92450 15.24750 9.392000 number of atom coordinates read : 3232 total number of charged atoms : 3086 net assigned charge : -7.999964 assigned positive charge : 471.0155 centred at (gu) : 86.02107 91.62429 95.08196 assigned negative charge : -479.0168 centred at (gu) : 85.45545 91.94024 95.54745 start vw surface at 0.1000000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 208426 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26656 grid for indexing accessible points = 1.400000 m= 106487 mr = 155840 m= 37428 mr = 87479 m= 9094 mr = 29914 m= 1255 mr = 6898 m= 54 mr = 786 m= 0 mr = 11 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 11118 time to turn everything in is 1.200000 number of dielectric boundary points 81816 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 24682 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) : 1.848199 object centre at (A) : 32.92450 15.24750 9.392000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4531390 -0.3835819 midg,1,midg; midg,igrid,midg -0.3340440 -0.3083772 1,midg,midg; igrid,midg,midg 0.1152114 0.7246003 gauss-seidel spectral radius is 0.9992700 estimated iterations to convergence 292 setup time was (sec) 1.510000 now iterating at: 11:38:00 rms-change max change #iterations 10.66076 300.5764 at 10iterations 6.296740 129.0761 at 20iterations 3.683750 74.13876 at 30iterations 2.148955 47.94603 at 40iterations 1.250721 25.19893 at 50iterations 0.7252280 12.42625 at 60iterations 0.4203903 7.826599 at 70iterations 0.2433456 3.959816 at 80iterations 0.1408970 2.351142 at 90iterations 8.1691548E-02 1.442764 at 100iterations 4.7217429E-02 0.8339388 at 110iterations 2.7356284E-02 0.4324312 at 120iterations 1.5889080E-02 0.3243990 at 130iterations 9.2150662E-03 0.1572609 at 140iterations 5.3970930E-03 9.4810486E-02 at 150iterations 3.2016137E-03 6.6268921E-02 at 160iterations 1.9409647E-03 3.3553600E-02 at 170iterations 1.2248921E-03 2.4772644E-02 at 180iterations finished qdiffx linear iterations at : 11:38:14 total time elapsed so far: 15.56000 # loops : 180 mean,max change (kT/e) : 1.2248921E-03 2.4772644E-02 energy calculations done at 15.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.69000 DelPhi exited at 11:38:15 15.693u 0.314s 0:16.36 97.7% 0+0k 0+0io 0pf+0w