Tue Nov 22 14:12:31 PST 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 Tue Nov 22 2011 at 14:12:36 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 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: 0.6018190 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): -34.67700 13.01900 ymin,ymax (A): 0.3950000 41.11900 zmin,zma (A): -4.4000030E-02 59.11000 x,y,z range (A): 47.69600 40.72400 59.15400 scale (grids/A): 0.6018190 object centre (A): -10.82900 20.75700 29.53300 number of atom coordinates read : 1946 total number of charged atoms : 1816 net assigned charge : 5.000010 assigned positive charge : 290.5820 centred at (gu) : 89.50523 89.70489 89.01163 assigned negative charge : -285.5823 centred at (gu) : 89.40533 89.85993 88.98543 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4744 nv = 96 ne = 84 npr = 39827 no. pairs analyzed = 39827 no. exposed pairs = 2411 no. arc points = 17306 no. surface atoms = 824 nbur = 1122 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 262 mr = 2599 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1786 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5845 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9027018E-09 2.4335556E-09 midg,1,midg; midg,igrid,midg 7.0643971E-09 -2.0424993E-09 1,midg,midg; igrid,midg,midg -6.6838646E-10 4.5519926E-09 gauss-seidel spectral radius is 0.9856554 estimated iterations to convergence 68 setup time was (sec) 0.4500000 now iterating at: 14:12:40 rms-change max change #iterations 9.7296372E-02 18.33183 at 10iterations 8.1444848E-03 1.452962 at 20iterations 6.9828349E-04 0.1266174 at 30iterations 6.0257204E-05 1.0448456E-02 at 40iterations 5.1012148E-06 9.5176697E-04 at 50iterations finished qdiffx linear iterations at : 14:12:48 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 5.1012148E-06 9.5176697E-04 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 14:12:51 3.296u 0.174s 0:15.28 22.6% 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 Tue Nov 22 2011 at 14:12:53 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 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: 1.805457 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): -34.67700 13.01900 ymin,ymax (A): 0.3950000 41.11900 zmin,zma (A): -4.4000030E-02 59.11000 x,y,z range (A): 47.69600 40.72400 59.15400 scale (grids/A): 1.805457 object centre (A): -10.82900 20.75700 29.53300 number of atom coordinates read : 1946 total number of charged atoms : 1816 net assigned charge : 5.000010 assigned positive charge : 290.5820 centred at (gu) : 88.51582 89.11474 87.03500 assigned negative charge : -285.5823 centred at (gu) : 88.21629 89.57985 86.95626 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 51584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17306 grid for indexing accessible points = 1.400000 m= 18419 mr = 35260 m= 2605 mr = 13797 m= 120 mr = 1630 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 638 time to turn everything in is 0.3800000 number of dielectric boundary points 22007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 14157 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) : 0.6018190 object centre at (A) : -10.82900 20.75700 29.53300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3962511E-02 2.3239199E-02 midg,1,midg; midg,igrid,midg 9.7631393E-03 -5.6357146E-03 1,midg,midg; igrid,midg,midg 5.2604162E-05 2.8435278E-03 gauss-seidel spectral radius is 0.9984046 estimated iterations to convergence 199 setup time was (sec) 0.6300000 now iterating at: 14:12:54 rms-change max change #iterations 3.265146 172.7648 at 10iterations 1.432797 55.41261 at 20iterations 0.6296774 26.01306 at 30iterations 0.2766195 13.21251 at 40iterations 0.1219185 5.125130 at 50iterations 5.3458314E-02 2.069847 at 60iterations 2.3669831E-02 0.9371090 at 70iterations 1.0367993E-02 0.3902311 at 80iterations 4.5789927E-03 0.1819954 at 90iterations 2.0046125E-03 7.5271606E-02 at 100iterations 8.8699179E-04 3.8977146E-02 at 110iterations 3.8989316E-04 1.5625000E-02 at 120iterations finished qdiffx linear iterations at : 14:13:03 total time elapsed so far: 6.530000 # loops : 120 mean,max change (kT/e) : 3.8989316E-04 1.5625000E-02 energy calculations done at 6.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.690000 DelPhi exited at 14:13:07 6.693u 0.168s 0:14.53 47.1% 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 Tue Nov 22 2011 at 14:13:09 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 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: 2.708185 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): -34.67700 13.01900 ymin,ymax (A): 0.3950000 41.11900 zmin,zma (A): -4.4000030E-02 59.11000 x,y,z range (A): 47.69600 40.72400 59.15400 scale (grids/A): 2.708185 object centre (A): -10.82900 20.75700 29.53300 number of atom coordinates read : 1946 total number of charged atoms : 1816 net assigned charge : 5.000010 assigned positive charge : 290.5820 centred at (gu) : 87.77371 88.67215 85.55248 assigned negative charge : -285.5823 centred at (gu) : 87.32442 89.36987 85.43443 start vw surface at 0.1200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 119337 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17306 grid for indexing accessible points = 1.400000 m= 60057 mr = 85424 m= 21111 mr = 49446 m= 4531 mr = 17329 m= 530 mr = 3369 m= 17 mr = 313 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 2113 time to turn everything in is 0.9400000 number of dielectric boundary points 49702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 14527 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) : 1.805457 object centre at (A) : -10.82900 20.75700 29.53300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8689025E-02 0.2123624 midg,1,midg; midg,igrid,midg 7.4138716E-02 -8.8620707E-02 1,midg,midg; igrid,midg,midg -3.5491746E-02 3.4295794E-02 gauss-seidel spectral radius is 0.9991758 estimated iterations to convergence 275 setup time was (sec) 1.240000 now iterating at: 14:13:16 rms-change max change #iterations 7.789825 260.7748 at 10iterations 4.376691 112.8584 at 20iterations 2.456065 54.98643 at 30iterations 1.362760 31.89817 at 40iterations 0.7597573 16.91845 at 50iterations 0.4212239 9.722931 at 60iterations 0.2338778 5.273855 at 70iterations 0.1305598 2.832269 at 80iterations 7.2395205E-02 1.632556 at 90iterations 4.0253717E-02 0.9144385 at 100iterations 2.2377947E-02 0.4811325 at 110iterations 1.2426953E-02 0.2598114 at 120iterations 6.8935412E-03 0.1472282 at 130iterations 3.8321665E-03 7.6604843E-02 at 140iterations 2.1276893E-03 4.5059204E-02 at 150iterations 1.1864305E-03 2.8102875E-02 at 160iterations 6.5819605E-04 1.3771057E-02 at 170iterations 3.6649656E-04 7.4768066E-03 at 180iterations finished qdiffx linear iterations at : 14:13:46 total time elapsed so far: 11.26000 # loops : 180 mean,max change (kT/e) : 3.6649656E-04 7.4768066E-03 energy calculations done at 11.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.43000 DelPhi exited at 14:13:57 11.430u 0.206s 0:48.95 23.7% 0+0k 0+0io 0pf+0w