Sat Oct 15 14:29:04 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 15 2011 at 14:29:05 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 = 2809 !!! WARNING: GLN 355 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6224756 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): -9.219000 47.97200 ymin,ymax (A): 4.144000 54.53200 zmin,zma (A): 7.406000 63.17000 x,y,z range (A): 57.19100 50.38800 55.76400 scale (grids/A): 0.6224756 object centre (A): 19.37650 29.33800 35.28800 number of atom coordinates read : 2809 total number of charged atoms : 2668 net assigned charge : -1.271969 assigned positive charge : 421.9012 centred at (gu) : 88.89912 89.30738 90.85604 assigned negative charge : -423.1743 centred at (gu) : 88.76344 89.47256 90.89247 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7401 nv = 96 ne = 84 npr = 55583 no. pairs analyzed = 55583 no. exposed pairs = 3757 no. arc points = 26760 no. surface atoms = 1268 nbur = 1541 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3787 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2648 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8931 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4733198E-09 -4.6727902E-09 midg,1,midg; midg,igrid,midg 1.3528032E-08 -1.2083985E-08 1,midg,midg; igrid,midg,midg -1.5008451E-08 7.3145121E-09 gauss-seidel spectral radius is 0.9866611 estimated iterations to convergence 71 setup time was (sec) 0.5700000 now iterating at: 14:29:05 rms-change max change #iterations 0.1313571 21.96010 at 10iterations 1.2066340E-02 1.586647 at 20iterations 1.1110499E-03 0.1436615 at 30iterations 1.0479451E-04 1.6174316E-02 at 40iterations 1.1078665E-05 2.2163391E-03 at 50iterations finished qdiffx linear iterations at : 14:29:09 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 1.1078665E-05 2.2163391E-03 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 14:29:10 4.243u 0.288s 0:04.97 90.9% 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 Sat Oct 15 2011 at 14:29:10 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 = 2809 !!! WARNING: GLN 355 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.867427 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): -9.219000 47.97200 ymin,ymax (A): 4.144000 54.53200 zmin,zma (A): 7.406000 63.17000 x,y,z range (A): 57.19100 50.38800 55.76400 scale (grids/A): 1.867427 object centre (A): 19.37650 29.33800 35.28800 number of atom coordinates read : 2809 total number of charged atoms : 2668 net assigned charge : -1.271969 assigned positive charge : 421.9012 centred at (gu) : 86.69643 87.92099 92.56709 assigned negative charge : -423.1743 centred at (gu) : 86.28999 88.41740 92.67688 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26760 grid for indexing accessible points = 1.400000 m= 26713 mr = 52787 m= 3860 mr = 18678 m= 208 mr = 2181 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 695 time to turn everything in is 0.6000000 number of dielectric boundary points 36479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 199 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20913 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) : 0.6224756 object centre at (A) : 19.37650 29.33800 35.28800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5934157E-04 7.6010724E-04 midg,1,midg; midg,igrid,midg 1.6357159E-02 -3.0190598E-02 1,midg,midg; igrid,midg,midg -5.3543162E-02 3.8813557E-02 gauss-seidel spectral radius is 0.9986157 estimated iterations to convergence 213 setup time was (sec) 0.9300000 now iterating at: 14:29:11 rms-change max change #iterations 4.282624 174.7862 at 10iterations 1.984747 70.96964 at 20iterations 0.9214602 27.66126 at 30iterations 0.4257570 13.54716 at 40iterations 0.1993543 6.481148 at 50iterations 9.2558883E-02 3.064232 at 60iterations 4.2909935E-02 1.487411 at 70iterations 2.0025192E-02 0.6027212 at 80iterations 9.2936410E-03 0.2802458 at 90iterations 4.3215752E-03 0.1262150 at 100iterations 2.0092216E-03 5.9739590E-02 at 110iterations 9.3981187E-04 2.9956818E-02 at 120iterations finished qdiffx linear iterations at : 14:29:19 total time elapsed so far: 9.660000 # loops : 120 mean,max change (kT/e) : 9.3981187E-04 2.9956818E-02 energy calculations done at 9.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.840000 DelPhi exited at 14:29:20 9.848u 0.267s 0:10.42 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 Sat Oct 15 2011 at 14:29:20 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 = 2809 !!! WARNING: GLN 355 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.801140 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): -9.219000 47.97200 ymin,ymax (A): 4.144000 54.53200 zmin,zma (A): 7.406000 63.17000 x,y,z range (A): 57.19100 50.38800 55.76400 scale (grids/A): 2.801140 object centre (A): 19.37650 29.33800 35.28800 number of atom coordinates read : 2809 total number of charged atoms : 2668 net assigned charge : -1.271969 assigned positive charge : 421.9012 centred at (gu) : 85.04462 86.88150 93.85046 assigned negative charge : -423.1743 centred at (gu) : 84.43492 87.62608 94.01526 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 183675 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26760 grid for indexing accessible points = 1.400000 m= 87645 mr = 128971 m= 29731 mr = 69280 m= 6464 mr = 22796 m= 784 mr = 4535 m= 39 mr = 496 m= 0 mr = 15 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 2027 time to turn everything in is 1.520000 number of dielectric boundary points 82245 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 21343 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) : 1.867427 object centre at (A) : 19.37650 29.33800 35.28800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2883498 0.1430796 midg,1,midg; midg,igrid,midg 0.1274176 -0.3171678 1,midg,midg; igrid,midg,midg -0.5602919 0.5098870 gauss-seidel spectral radius is 0.9992753 estimated iterations to convergence 293 setup time was (sec) 1.870000 now iterating at: 14:29:22 rms-change max change #iterations 10.33269 340.1334 at 10iterations 6.166995 187.7739 at 20iterations 3.632491 74.60907 at 30iterations 2.129120 42.38026 at 40iterations 1.246667 24.33421 at 50iterations 0.7260404 15.56963 at 60iterations 0.4218179 9.889610 at 70iterations 0.2444537 4.791769 at 80iterations 0.1419362 2.656484 at 90iterations 8.2204796E-02 1.505994 at 100iterations 4.7625102E-02 0.9438462 at 110iterations 2.7553532E-02 0.5271938 at 120iterations 1.5933413E-02 0.2899141 at 130iterations 9.2087016E-03 0.1601639 at 140iterations 5.3110747E-03 0.1034412 at 150iterations 3.0739496E-03 5.7901382E-02 at 160iterations 1.7760773E-03 3.2803535E-02 at 170iterations 1.0247611E-03 1.8669128E-02 at 180iterations finished qdiffx linear iterations at : 14:29:36 total time elapsed so far: 15.82000 # loops : 180 mean,max change (kT/e) : 1.0247611E-03 1.8669128E-02 energy calculations done at 15.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.01000 DelPhi exited at 14:29:37 16.008u 0.284s 0:16.83 96.7% 0+0k 0+0io 0pf+0w