Mon Oct 10 11:33:27 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 Mon Oct 10 2011 at 11:33:27 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: ASL 106 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6647248 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): 6.513000 55.51600 ymin,ymax (A): -69.34200 -21.06200 zmin,zma (A): 33.13200 86.68800 x,y,z range (A): 49.00300 48.28000 53.55600 scale (grids/A): 0.6647248 object centre (A): 31.01450 -45.20200 59.91000 number of atom coordinates read : 2136 total number of charged atoms : 1995 net assigned charge : -8.199974 assigned positive charge : 323.1318 centred at (gu) : 91.61704 88.21125 91.77850 assigned negative charge : -331.3319 centred at (gu) : 91.74985 88.12881 91.53844 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6310 nv = 96 ne = 84 npr = 43587 no. pairs analyzed = 43587 no. exposed pairs = 2724 no. arc points = 19270 no. surface atoms = 912 nbur = 1224 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3384 m= 0 mr = 63 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 121 time to turn everything in is 0.2400000 number of dielectric boundary points 3219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1793 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7350 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8573689E-08 3.0890543E-08 midg,1,midg; midg,igrid,midg -5.6655214E-08 -5.8973493E-09 1,midg,midg; igrid,midg,midg 5.5034532E-10 -6.8387287E-08 gauss-seidel spectral radius is 0.9882280 estimated iterations to convergence 75 setup time was (sec) 0.4700000 now iterating at: 11:33:28 rms-change max change #iterations 0.1631467 25.93035 at 10iterations 1.7344097E-02 2.610474 at 20iterations 1.8664483E-03 0.2555504 at 30iterations 1.9687394E-04 3.0632973E-02 at 40iterations 2.1425922E-05 4.0779114E-03 at 50iterations finished qdiffx linear iterations at : 11:33:31 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 2.1425922E-05 4.0779114E-03 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 11:33:31 3.284u 0.210s 0:03.76 92.8% 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 Mon Oct 10 2011 at 11:33:31 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: ASL 106 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.994174 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): 6.513000 55.51600 ymin,ymax (A): -69.34200 -21.06200 zmin,zma (A): 33.13200 86.68800 x,y,z range (A): 49.00300 48.28000 53.55600 scale (grids/A): 1.994174 object centre (A): 31.01450 -45.20200 59.91000 number of atom coordinates read : 2136 total number of charged atoms : 1995 net assigned charge : -8.199974 assigned positive charge : 323.1318 centred at (gu) : 94.85098 84.63370 95.33532 assigned negative charge : -331.3319 centred at (gu) : 95.24953 84.38636 94.61518 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 67709 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19270 grid for indexing accessible points = 1.400000 m= 24562 mr = 46036 m= 4029 mr = 17969 m= 280 mr = 2503 m= 1 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 3276 time to turn everything in is 0.5000000 number of dielectric boundary points 29965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 15754 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) : 0.6647248 object centre at (A) : 31.01450 -45.20200 59.91000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4180922E-02 -1.1370125E-02 midg,1,midg; midg,igrid,midg -1.6112005E-02 2.4598581E-03 1,midg,midg; igrid,midg,midg -4.2647296E-03 -4.7877561E-02 gauss-seidel spectral radius is 0.9987003 estimated iterations to convergence 220 setup time was (sec) 0.7600000 now iterating at: 11:33:32 rms-change max change #iterations 4.261039 168.6794 at 10iterations 2.033695 79.85918 at 20iterations 0.9659823 34.00903 at 30iterations 0.4611414 15.41412 at 40iterations 0.2196708 7.260910 at 50iterations 0.1045372 3.451639 at 60iterations 4.9873184E-02 1.550735 at 70iterations 2.3743670E-02 0.7796059 at 80iterations 1.1317649E-02 0.3420734 at 90iterations 5.3844694E-03 0.1646843 at 100iterations 2.5730839E-03 8.4579468E-02 at 110iterations 1.2234639E-03 3.9334655E-02 at 120iterations finished qdiffx linear iterations at : 11:33:38 total time elapsed so far: 6.650000 # loops : 120 mean,max change (kT/e) : 1.2234639E-03 3.9334655E-02 energy calculations done at 6.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.800000 DelPhi exited at 11:33:39 6.802u 0.203s 0:07.34 95.3% 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 Mon Oct 10 2011 at 11:33:39 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: ASL 106 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.991262 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): 6.513000 55.51600 ymin,ymax (A): -69.34200 -21.06200 zmin,zma (A): 33.13200 86.68800 x,y,z range (A): 49.00300 48.28000 53.55600 scale (grids/A): 2.991262 object centre (A): 31.01450 -45.20200 59.91000 number of atom coordinates read : 2136 total number of charged atoms : 1995 net assigned charge : -8.199974 assigned positive charge : 323.1318 centred at (gu) : 97.27638 81.95046 98.00295 assigned negative charge : -331.3319 centred at (gu) : 97.87415 81.57945 96.92263 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 156209 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19270 grid for indexing accessible points = 1.400000 m= 78761 mr = 111510 m= 29152 mr = 64115 m= 7395 mr = 23267 m= 1255 mr = 5591 m= 102 mr = 848 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 11014 time to turn everything in is 1.190000 number of dielectric boundary points 67496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 15960 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) : 1.994174 object centre at (A) : 31.01450 -45.20200 59.91000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3214509 -2.3870979E-02 midg,1,midg; midg,igrid,midg -9.0395205E-02 -8.5572188E-04 1,midg,midg; igrid,midg,midg -4.8458368E-02 -0.4068112 gauss-seidel spectral radius is 0.9992704 estimated iterations to convergence 292 setup time was (sec) 1.460000 now iterating at: 11:33:40 rms-change max change #iterations 9.883333 377.2325 at 10iterations 5.757600 141.9395 at 20iterations 3.341382 75.21981 at 30iterations 1.934529 37.64544 at 40iterations 1.116751 21.64745 at 50iterations 0.6445040 11.92096 at 60iterations 0.3716212 6.715988 at 70iterations 0.2146557 3.992355 at 80iterations 0.1237444 2.378478 at 90iterations 7.1306102E-02 1.486469 at 100iterations 4.1103818E-02 0.7395849 at 110iterations 2.3629308E-02 0.4420166 at 120iterations 1.3643840E-02 0.2568951 at 130iterations 7.8475727E-03 0.1439476 at 140iterations 4.5186863E-03 8.9483261E-02 at 150iterations 2.6057516E-03 4.9949646E-02 at 160iterations 1.4991652E-03 2.6304245E-02 at 170iterations 8.6340163E-04 1.6510487E-02 at 180iterations finished qdiffx linear iterations at : 11:33:50 total time elapsed so far: 10.69000 # loops : 180 mean,max change (kT/e) : 8.6340163E-04 1.6510487E-02 energy calculations done at 10.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.87000 DelPhi exited at 11:33:50 10.876u 0.164s 0:11.44 96.4% 0+0k 0+0io 0pf+0w