Sun Oct 9 02:51:39 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 Sun Oct 9 2011 at 02:51:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2511 !!! WARNING: MG4 428 has a net charge of 1.4000 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: 0.6227042 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): -40.86800 16.30200 ymin,ymax (A): -21.07100 27.49200 zmin,zma (A): -53.23300 -0.1090001 x,y,z range (A): 57.17000 48.56300 53.12400 scale (grids/A): 0.6227042 object centre (A): -12.28300 3.210500 -26.67100 number of atom coordinates read : 2511 total number of charged atoms : 2377 net assigned charge : -1.599991 assigned positive charge : 381.3471 centred at (gu) : 88.66497 90.10654 90.82279 assigned negative charge : -382.9478 centred at (gu) : 88.63328 90.13042 90.82356 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6429 nv = 96 ne = 84 npr = 50719 no. pairs analyzed = 50719 no. exposed pairs = 3101 no. arc points = 21819 no. surface atoms = 1029 nbur = 1482 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 299 mr = 3503 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 198 time to turn everything in is 0.2800000 number of dielectric boundary points 3202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2178 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7922 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0974230E-09 -1.6846549E-09 midg,1,midg; midg,igrid,midg 3.1657621E-10 -3.1250751E-09 1,midg,midg; igrid,midg,midg -4.8480371E-09 6.3467698E-10 gauss-seidel spectral radius is 0.9866369 estimated iterations to convergence 71 setup time was (sec) 0.5000000 now iterating at: 02:51:40 rms-change max change #iterations 0.1260744 18.89997 at 10iterations 1.1704866E-02 1.766315 at 20iterations 1.0862151E-03 0.1635787 at 30iterations 1.0232374E-04 1.5369415E-02 at 40iterations 9.4670650E-06 1.3580322E-03 at 50iterations finished qdiffx linear iterations at : 02:51:42 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 9.4670650E-06 1.3580322E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 02:51:43 3.099u 0.118s 0:03.51 91.1% 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 Sun Oct 9 2011 at 02:51:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2511 !!! WARNING: MG4 428 has a net charge of 1.4000 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: 1.868113 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): -40.86800 16.30200 ymin,ymax (A): -21.07100 27.49200 zmin,zma (A): -53.23300 -0.1090001 x,y,z range (A): 57.17000 48.56300 53.12400 scale (grids/A): 1.868113 object centre (A): -12.28300 3.210500 -26.67100 number of atom coordinates read : 2511 total number of charged atoms : 2377 net assigned charge : -1.599991 assigned positive charge : 381.3471 centred at (gu) : 85.99444 90.31925 92.46773 assigned negative charge : -382.9478 centred at (gu) : 85.89973 90.39092 92.47064 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70315 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21819 grid for indexing accessible points = 1.400000 m= 23961 mr = 48419 m= 3348 mr = 17498 m= 144 mr = 2041 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 6308 time to turn everything in is 0.4800000 number of dielectric boundary points 29768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 18627 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) : 0.6227042 object centre at (A) : -12.28300 3.210500 -26.67100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6733059E-04 1.2384577E-03 midg,1,midg; midg,igrid,midg 3.3924130E-03 -9.6240779E-03 1,midg,midg; igrid,midg,midg -7.1872198E-03 2.5181025E-02 gauss-seidel spectral radius is 0.9985768 estimated iterations to convergence 210 setup time was (sec) 0.7400000 now iterating at: 02:51:43 rms-change max change #iterations 4.060288 173.2567 at 10iterations 1.863857 65.32140 at 20iterations 0.8571517 28.88894 at 30iterations 0.3960578 13.02247 at 40iterations 0.1821361 6.333260 at 50iterations 8.3918914E-02 2.852692 at 60iterations 3.8635686E-02 1.297632 at 70iterations 1.7765587E-02 0.5902152 at 80iterations 8.2160681E-03 0.2897263 at 90iterations 3.7869727E-03 0.1203529 at 100iterations 1.7456233E-03 5.5908203E-02 at 110iterations 8.0457883E-04 2.7388573E-02 at 120iterations finished qdiffx linear iterations at : 02:51:49 total time elapsed so far: 6.810000 # loops : 120 mean,max change (kT/e) : 8.0457883E-04 2.7388573E-02 energy calculations done at 6.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.980000 DelPhi exited at 02:51:50 6.984u 0.164s 0:07.47 95.5% 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 02:51:50 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 = 2511 !!! WARNING: MG4 428 has a net charge of 1.4000 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: 2.802169 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): -40.86800 16.30200 ymin,ymax (A): -21.07100 27.49200 zmin,zma (A): -53.23300 -0.1090001 x,y,z range (A): 57.17000 48.56300 53.12400 scale (grids/A): 2.802169 object centre (A): -12.28300 3.210500 -26.67100 number of atom coordinates read : 2511 total number of charged atoms : 2377 net assigned charge : -1.599991 assigned positive charge : 381.3471 centred at (gu) : 83.99155 90.47874 93.70143 assigned negative charge : -382.9478 centred at (gu) : 83.84955 90.58635 93.70589 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 162827 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21819 grid for indexing accessible points = 1.400000 m= 79104 mr = 117726 m= 26734 mr = 64240 m= 5782 mr = 21371 m= 692 mr = 4308 m= 21 mr = 464 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 21261 time to turn everything in is 1.160000 number of dielectric boundary points 67042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 19015 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) : 1.868113 object centre at (A) : -12.28300 3.210500 -26.67100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3817049E-02 0.1015198 midg,1,midg; midg,igrid,midg 5.6895901E-02 -0.1585803 1,midg,midg; igrid,midg,midg -0.1728013 0.3329947 gauss-seidel spectral radius is 0.9992436 estimated iterations to convergence 287 setup time was (sec) 1.440000 now iterating at: 02:51:52 rms-change max change #iterations 9.674791 297.3136 at 10iterations 5.661946 153.0096 at 20iterations 3.281601 90.74307 at 30iterations 1.901982 44.18453 at 40iterations 1.095301 25.89156 at 50iterations 0.6305292 13.23594 at 60iterations 0.3630303 7.837793 at 70iterations 0.2081288 4.494178 at 80iterations 0.1189660 2.531132 at 90iterations 6.8229966E-02 1.412060 at 100iterations 3.9057966E-02 0.7619171 at 110iterations 2.2354878E-02 0.4660279 at 120iterations 1.2784787E-02 0.2763042 at 130iterations 7.3191151E-03 0.1428945 at 140iterations 4.1764569E-03 8.4633827E-02 at 150iterations 2.3863355E-03 5.0791740E-02 at 160iterations 1.3627594E-03 3.0897141E-02 at 170iterations 7.7875861E-04 1.5563965E-02 at 180iterations finished qdiffx linear iterations at : 02:52:01 total time elapsed so far: 10.88000 # loops : 180 mean,max change (kT/e) : 7.7875861E-04 1.5563965E-02 energy calculations done at 10.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.06000 DelPhi exited at 02:52:02 11.062u 0.170s 0:11.55 97.2% 0+0k 0+0io 0pf+0w