Sun Oct 9 16:09:08 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 16:09:08 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3061 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: GLM 240 has a net charge of -0.0940 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: 0.6345924 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): -15.54900 36.73800 ymin,ymax (A): 55.34800 107.8050 zmin,zma (A): -4.272000 51.82700 x,y,z range (A): 52.28700 52.45700 56.09900 scale (grids/A): 0.6345924 object centre (A): 10.59450 81.57650 23.77750 number of atom coordinates read : 3061 total number of charged atoms : 2909 net assigned charge : -4.687975 assigned positive charge : 450.7791 centred at (gu) : 90.36008 88.50684 91.41753 assigned negative charge : -455.4685 centred at (gu) : 90.40102 88.37014 91.45285 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8181 nv = 96 ne = 84 npr = 63186 no. pairs analyzed = 63186 no. exposed pairs = 3787 no. arc points = 26114 no. surface atoms = 1292 nbur = 1769 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 469 mr = 4474 m= 2 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2536 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9954 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0344009E-09 -1.3018786E-08 midg,1,midg; midg,igrid,midg -3.0132934E-08 7.4147217E-09 1,midg,midg; igrid,midg,midg -6.3088978E-10 -1.1090036E-08 gauss-seidel spectral radius is 0.9871759 estimated iterations to convergence 72 setup time was (sec) 0.5500000 now iterating at: 16:09:08 rms-change max change #iterations 0.1557418 23.30357 at 10iterations 1.5065654E-02 1.922012 at 20iterations 1.4614473E-03 0.1906739 at 30iterations 1.4641855E-04 2.0317078E-02 at 40iterations 1.6243994E-05 2.5024414E-03 at 50iterations finished qdiffx linear iterations at : 16:09:11 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.6243994E-05 2.5024414E-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) 3.390000 DelPhi exited at 16:09:12 3.392u 0.217s 0:03.91 92.0% 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 16:09:12 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3061 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: GLM 240 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.903777 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): -15.54900 36.73800 ymin,ymax (A): 55.34800 107.8050 zmin,zma (A): -4.272000 51.82700 x,y,z range (A): 52.28700 52.45700 56.09900 scale (grids/A): 1.903777 object centre (A): 10.59450 81.57650 23.77750 number of atom coordinates read : 3061 total number of charged atoms : 2909 net assigned charge : -4.687975 assigned positive charge : 450.7791 centred at (gu) : 91.07963 85.51965 94.25190 assigned negative charge : -455.4685 centred at (gu) : 91.20293 85.11016 94.35827 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 88661 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26114 grid for indexing accessible points = 1.400000 m= 32336 mr = 61988 m= 5453 mr = 23386 m= 351 mr = 3467 m= 3 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 73 time to turn everything in is 0.6400000 number of dielectric boundary points 37852 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22849 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) : 0.6345924 object centre at (A) : 10.59450 81.57650 23.77750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1689724E-02 2.4253519E-03 midg,1,midg; midg,igrid,midg -3.7965026E-02 -9.2345178E-03 1,midg,midg; igrid,midg,midg -3.9068200E-02 -3.1596556E-02 gauss-seidel spectral radius is 0.9986748 estimated iterations to convergence 218 setup time was (sec) 0.9100000 now iterating at: 16:09:13 rms-change max change #iterations 4.648204 206.2607 at 10iterations 2.195381 76.37315 at 20iterations 1.037809 30.56380 at 30iterations 0.4909755 15.34903 at 40iterations 0.2329224 6.951679 at 50iterations 0.1105294 3.457607 at 60iterations 5.2402891E-02 1.485525 at 70iterations 2.4766074E-02 0.7160511 at 80iterations 1.1734234E-02 0.3506012 at 90iterations 5.5678179E-03 0.1792836 at 100iterations 2.6369253E-03 7.4400425E-02 at 110iterations 1.2522793E-03 3.5346985E-02 at 120iterations finished qdiffx linear iterations at : 16:09:21 total time elapsed so far: 8.880000 # loops : 120 mean,max change (kT/e) : 1.2522793E-03 3.5346985E-02 energy calculations done at 8.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.060000 DelPhi exited at 16:09:21 9.059u 0.278s 0:09.61 96.9% 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 16:09:21 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3061 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: GLM 240 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.855666 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): -15.54900 36.73800 ymin,ymax (A): 55.34800 107.8050 zmin,zma (A): -4.272000 51.82700 x,y,z range (A): 52.28700 52.45700 56.09900 scale (grids/A): 2.855666 object centre (A): 10.59450 81.57650 23.77750 number of atom coordinates read : 3061 total number of charged atoms : 2909 net assigned charge : -4.687975 assigned positive charge : 450.7791 centred at (gu) : 91.61935 83.27936 96.37764 assigned negative charge : -455.4685 centred at (gu) : 91.80441 82.66518 96.53742 start vw surface at 0.1900000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 205159 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26114 grid for indexing accessible points = 1.400000 m= 103292 mr = 150507 m= 38904 mr = 83706 m= 10093 mr = 30785 m= 1486 mr = 7560 m= 81 mr = 991 m= 0 mr = 29 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 223 time to turn everything in is 1.630000 number of dielectric boundary points 85437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 23271 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) : 1.903777 object centre at (A) : 10.59450 81.57650 23.77750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5114968 7.7043936E-02 midg,1,midg; midg,igrid,midg -0.4042313 -0.2529723 1,midg,midg; igrid,midg,midg -0.5496103 -0.3692250 gauss-seidel spectral radius is 0.9992802 estimated iterations to convergence 294 setup time was (sec) 1.960000 now iterating at: 16:09:23 rms-change max change #iterations 10.89345 407.8206 at 10iterations 6.428774 150.4237 at 20iterations 3.757727 74.32362 at 30iterations 2.203631 44.31938 at 40iterations 1.287699 24.17139 at 50iterations 0.7498075 13.85788 at 60iterations 0.4368847 8.530963 at 70iterations 0.2537816 4.402449 at 80iterations 0.1476731 2.583332 at 90iterations 8.5877031E-02 1.697858 at 100iterations 4.9888454E-02 0.9794559 at 110iterations 2.8929401E-02 0.5204468 at 120iterations 1.6822608E-02 0.2943945 at 130iterations 9.7538410E-03 0.1679659 at 140iterations 5.6595840E-03 9.6618652E-02 at 150iterations 3.2787328E-03 5.7281852E-02 at 160iterations 1.9018401E-03 3.3911705E-02 at 170iterations 1.1062939E-03 1.9869804E-02 at 180iterations finished qdiffx linear iterations at : 16:09:34 total time elapsed so far: 13.01000 # loops : 180 mean,max change (kT/e) : 1.1062939E-03 1.9869804E-02 energy calculations done at 13.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.19000 DelPhi exited at 16:09:35 13.192u 0.257s 0:13.84 97.1% 0+0k 0+0io 0pf+0w