Tue Oct 11 08:18:38 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 Tue Oct 11 2011 at 08:18:38 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 = 3113 !!! WARNING: ASN 491 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5771164 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): 96.06800 150.2160 ymin,ymax (A): -14.68900 42.07200 zmin,zma (A): 5.517000 67.20300 x,y,z range (A): 54.14799 56.76100 61.68600 scale (grids/A): 0.5771164 object centre (A): 123.1420 13.69150 36.36000 number of atom coordinates read : 3113 total number of charged atoms : 2975 net assigned charge : -6.271975 assigned positive charge : 461.9230 centred at (gu) : 90.98724 89.31695 89.93022 assigned negative charge : -468.1960 centred at (gu) : 90.95598 89.28981 89.97755 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6756 nv = 96 ne = 84 npr = 63955 no. pairs analyzed = 63955 no. exposed pairs = 3962 no. arc points = 27320 no. surface atoms = 1331 nbur = 1782 mkacc time = 0.1600000 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 = 1.484000 m= 316 mr = 3578 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3483 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2858 ## 322 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8736 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5404612E-10 -2.2065902E-09 midg,1,midg; midg,igrid,midg -2.1262900E-09 -5.7931704E-10 1,midg,midg; igrid,midg,midg -1.5144059E-09 -7.2483664E-10 gauss-seidel spectral radius is 0.9845143 estimated iterations to convergence 66 setup time was (sec) 0.5900000 now iterating at: 08:18:39 rms-change max change #iterations 9.9688143E-02 16.35129 at 10iterations 7.7274423E-03 1.144966 at 20iterations 8.5348974E-04 0.1317439 at 30iterations 2.1641034E-04 3.2094002E-02 at 40iterations 7.2929528E-05 1.1107445E-02 at 50iterations finished qdiffx linear iterations at : 08:18:42 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 7.2929528E-05 1.1107445E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 08:18:42 3.375u 0.144s 0:03.91 89.7% 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 08:18:42 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 = 3113 !!! WARNING: ASN 491 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.731349 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): 96.06800 150.2160 ymin,ymax (A): -14.68900 42.07200 zmin,zma (A): 5.517000 67.20300 x,y,z range (A): 54.14799 56.76100 61.68600 scale (grids/A): 1.731349 object centre (A): 123.1420 13.69150 36.36000 number of atom coordinates read : 3113 total number of charged atoms : 2975 net assigned charge : -6.271975 assigned positive charge : 461.9230 centred at (gu) : 92.96127 87.95030 89.78981 assigned negative charge : -468.1960 centred at (gu) : 92.86755 87.86912 89.93266 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 74084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27320 grid for indexing accessible points = 1.400000 m= 25082 mr = 50660 m= 3216 mr = 17693 m= 119 mr = 1743 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1323 time to turn everything in is 0.5600000 number of dielectric boundary points 32388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 286 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 23074 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) : 0.5771164 object centre at (A) : 123.1420 13.69150 36.36000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5792874E-02 -3.3152003E-02 midg,1,midg; midg,igrid,midg -8.4519414E-03 2.8744226E-03 1,midg,midg; igrid,midg,midg -1.1753892E-02 3.7801282E-03 gauss-seidel spectral radius is 0.9984058 estimated iterations to convergence 199 setup time was (sec) 0.8500000 now iterating at: 08:18:43 rms-change max change #iterations 3.855192 179.0441 at 10iterations 1.695232 60.17566 at 20iterations 0.7435189 25.38950 at 30iterations 0.3286484 10.34056 at 40iterations 0.1446205 4.531200 at 50iterations 6.3868217E-02 2.391140 at 60iterations 2.8091148E-02 0.9502831 at 70iterations 1.2420170E-02 0.3949986 at 80iterations 5.5282242E-03 0.1958590 at 90iterations 2.5071402E-03 9.4567597E-02 at 100iterations 1.1799646E-03 5.1204681E-02 at 110iterations 5.8278017E-04 2.0916700E-02 at 120iterations finished qdiffx linear iterations at : 08:18:50 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 5.8278017E-04 2.0916700E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 08:18:50 7.623u 0.191s 0:08.14 95.9% 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 Tue Oct 11 2011 at 08:18:50 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 = 3113 !!! WARNING: ASN 491 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.597024 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): 96.06800 150.2160 ymin,ymax (A): -14.68900 42.07200 zmin,zma (A): 5.517000 67.20300 x,y,z range (A): 54.14799 56.76100 61.68600 scale (grids/A): 2.597024 object centre (A): 123.1420 13.69150 36.36000 number of atom coordinates read : 3113 total number of charged atoms : 2975 net assigned charge : -6.271975 assigned positive charge : 461.9230 centred at (gu) : 94.44165 86.92516 89.68433 assigned negative charge : -468.1960 centred at (gu) : 94.30111 86.80346 89.89878 start vw surface at 0.2100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 171397 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27320 grid for indexing accessible points = 1.400000 m= 83582 mr = 123310 m= 27247 mr = 66876 m= 5387 mr = 21010 m= 504 mr = 3724 m= 7 mr = 243 m= 0 mr = 2 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 4770 time to turn everything in is 1.420000 number of dielectric boundary points 72959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 23789 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) : 1.731349 object centre at (A) : 123.1420 13.69150 36.36000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3445512 -0.3787150 midg,1,midg; midg,igrid,midg 5.7737142E-02 2.1676011E-02 1,midg,midg; igrid,midg,midg -0.2231928 0.1302477 gauss-seidel spectral radius is 0.9992083 estimated iterations to convergence 281 setup time was (sec) 1.730000 now iterating at: 08:18:52 rms-change max change #iterations 9.567704 294.1086 at 10iterations 5.559927 151.6392 at 20iterations 3.187515 69.02626 at 30iterations 1.828939 37.48669 at 40iterations 1.039543 20.22264 at 50iterations 0.5911525 12.36042 at 60iterations 0.3360869 6.816452 at 70iterations 0.1904427 4.404766 at 80iterations 0.1076411 2.212709 at 90iterations 6.1004724E-02 1.178321 at 100iterations 3.4579203E-02 0.6332970 at 110iterations 1.9468645E-02 0.3907967 at 120iterations 1.1066605E-02 0.2231672 at 130iterations 6.2792548E-03 0.1179981 at 140iterations 3.5752822E-03 6.9777489E-02 at 150iterations 2.0579260E-03 4.0240288E-02 at 160iterations 1.2058752E-03 2.2602081E-02 at 170iterations 7.2831771E-04 1.4912605E-02 at 180iterations finished qdiffx linear iterations at : 08:19:02 total time elapsed so far: 11.84000 # loops : 180 mean,max change (kT/e) : 7.2831771E-04 1.4912605E-02 energy calculations done at 11.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 08:19:03 12.029u 0.176s 0:12.71 95.9% 0+0k 0+0io 0pf+0w