Tue Oct 11 03:14:43 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 Tue Oct 11 2011 at 03:14:43 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2172 !!! WARNING: ASL 306 has a net charge of -0.1000 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: 0.7119288 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): 19.30400 66.56800 ymin,ymax (A): 16.42000 61.19400 zmin,zma (A): 4.610000 54.61500 x,y,z range (A): 47.26400 44.77400 50.00500 scale (grids/A): 0.7119288 object centre (A): 42.93600 38.80700 29.61250 number of atom coordinates read : 2172 total number of charged atoms : 2046 net assigned charge : 1.900011 assigned positive charge : 322.8015 centred at (gu) : 90.70465 90.66196 90.38866 assigned negative charge : -320.9019 centred at (gu) : 90.65037 90.71243 90.59353 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7491 nv = 96 ne = 84 npr = 45398 no. pairs analyzed = 45398 no. exposed pairs = 2776 no. arc points = 19357 no. surface atoms = 927 nbur = 1245 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 518 mr = 4126 m= 6 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1661 ## 117 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8297 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2147736E-07 -1.0702514E-07 midg,1,midg; midg,igrid,midg 4.1007429E-08 -1.1636994E-08 1,midg,midg; igrid,midg,midg -1.0498261E-08 5.5906352E-08 gauss-seidel spectral radius is 0.9897299 estimated iterations to convergence 80 setup time was (sec) 0.6100000 now iterating at: 03:14:44 rms-change max change #iterations 0.2155834 29.19722 at 10iterations 2.6384128E-02 3.832619 at 20iterations 3.3607630E-03 0.4302349 at 30iterations 4.4864841E-04 6.4508438E-02 at 40iterations 6.7085799E-05 9.0141296E-03 at 50iterations finished qdiffx linear iterations at : 03:14:49 total time elapsed so far: 4.850000 # loops : 50 mean,max change (kT/e) : 6.7085799E-05 9.0141296E-03 energy calculations done at 4.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.010000 DelPhi exited at 03:14:49 5.017u 0.441s 0:05.81 93.8% 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 Oct 11 2011 at 03:14:49 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2172 !!! WARNING: ASL 306 has a net charge of -0.1000 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: 2.135787 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): 19.30400 66.56800 ymin,ymax (A): 16.42000 61.19400 zmin,zma (A): 4.610000 54.61500 x,y,z range (A): 47.26400 44.77400 50.00500 scale (grids/A): 2.135787 object centre (A): 42.93600 38.80700 29.61250 number of atom coordinates read : 2172 total number of charged atoms : 2046 net assigned charge : 1.900011 assigned positive charge : 322.8015 centred at (gu) : 92.11380 91.98571 91.16602 assigned negative charge : -320.9019 centred at (gu) : 91.95089 92.13743 91.78042 start vw surface at 0.1000000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19357 grid for indexing accessible points = 1.400000 m= 30826 mr = 55207 m= 6335 mr = 22886 m= 656 mr = 4128 m= 28 mr = 298 m= 0 mr = 1 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 34811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 16236 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) : 0.7119288 object centre at (A) : 42.93600 38.80700 29.61250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3548526E-02 -7.4433528E-02 midg,1,midg; midg,igrid,midg 1.8703757E-02 -1.3402585E-02 1,midg,midg; igrid,midg,midg -3.4222137E-02 -4.3798413E-02 gauss-seidel spectral radius is 0.9988620 estimated iterations to convergence 235 setup time was (sec) 1.020000 now iterating at: 03:14:51 rms-change max change #iterations 4.799139 207.8414 at 10iterations 2.399778 79.83916 at 20iterations 1.206221 39.36792 at 30iterations 0.6045641 18.72677 at 40iterations 0.3029897 8.856634 at 50iterations 0.1518530 4.513973 at 60iterations 7.6085821E-02 2.145935 at 70iterations 3.8106792E-02 1.128899 at 80iterations 1.9072892E-02 0.5635147 at 90iterations 9.5751965E-03 0.2914391 at 100iterations 4.8045674E-03 0.1349373 at 110iterations 2.4183148E-03 6.8254471E-02 at 120iterations finished qdiffx linear iterations at : 03:15:02 total time elapsed so far: 11.96000 # loops : 120 mean,max change (kT/e) : 2.4183148E-03 6.8254471E-02 energy calculations done at 11.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.13000 DelPhi exited at 03:15:02 12.133u 0.491s 0:12.90 97.8% 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 Oct 11 2011 at 03:15:02 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2172 !!! WARNING: ASL 306 has a net charge of -0.1000 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: 3.203680 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): 19.30400 66.56800 ymin,ymax (A): 16.42000 61.19400 zmin,zma (A): 4.610000 54.61500 x,y,z range (A): 47.26400 44.77400 50.00500 scale (grids/A): 3.203680 object centre (A): 42.93600 38.80700 29.61250 number of atom coordinates read : 2172 total number of charged atoms : 2046 net assigned charge : 1.900011 assigned positive charge : 322.8015 centred at (gu) : 93.17049 92.97847 91.74901 assigned negative charge : -320.9019 centred at (gu) : 92.92630 93.20609 92.67058 start vw surface at 0.1100000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 183875 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19357 grid for indexing accessible points = 1.400000 m= 94912 mr = 133813 m= 39556 mr = 77637 m= 12028 mr = 32253 m= 2538 mr = 9056 m= 277 mr = 1764 m= 10 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.110000 number of dielectric boundary points 78538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 16368 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) : 2.135787 object centre at (A) : 42.93600 38.80700 29.61250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3644243 -0.8628038 midg,1,midg; midg,igrid,midg 0.1152658 -0.1685183 1,midg,midg; igrid,midg,midg -0.3035929 -0.5204938 gauss-seidel spectral radius is 0.9993191 estimated iterations to convergence 302 setup time was (sec) 2.490000 now iterating at: 03:15:05 rms-change max change #iterations 10.56642 364.6354 at 10iterations 6.267299 132.0279 at 20iterations 3.707870 67.52184 at 30iterations 2.193859 43.73225 at 40iterations 1.296084 23.36780 at 50iterations 0.7661373 17.63168 at 60iterations 0.4506825 7.869291 at 70iterations 0.2664081 4.655451 at 80iterations 0.1565582 2.702635 at 90iterations 9.1917992E-02 1.570086 at 100iterations 5.4126859E-02 0.9217412 at 110iterations 3.1780005E-02 0.5392723 at 120iterations 1.8749284E-02 0.2871161 at 130iterations 1.1000255E-02 0.1810603 at 140iterations 6.4718048E-03 0.1106606 at 150iterations 3.8080884E-03 6.1349869E-02 at 160iterations 2.2455161E-03 3.8594246E-02 at 170iterations 1.3248364E-03 2.3651123E-02 at 180iterations finished qdiffx linear iterations at : 03:15:24 total time elapsed so far: 21.07000 # loops : 180 mean,max change (kT/e) : 1.3248364E-03 2.3651123E-02 energy calculations done at 21.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.24000 DelPhi exited at 03:15:24 21.242u 0.526s 0:22.32 97.4% 0+0k 0+0io 0pf+0w