error in combine select of xyz for protein and RNA moleules

hii i perfomed the following steps.

print(pdbfile)

Call: read.pdb(file = "smallwt1.pdb")

Total Models#: 1 Total Atoms#: 2984, XYZs#: 8952 Chains#: 1 (values: A)

 Protein Atoms#: 1462  (residues/Calpha atoms#: 94)
 Nucleic acid Atoms#: 1522  (residues/phosphate atoms#: 48)

 Non-protein/nucleic Atoms#: 0  (residues: 0)
 Non-protein/nucleic resid values: [ none ]

Protein sequence: GSSGSSGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGV AFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI

Nucleic acid sequence: AUUAAAGACCAACCAACUUCUGUUCUCUAAACGAACUUUAAAUUAAUA

attr: atom, xyz, calpha, call

dcd <- read.dcd(dcdfile) NATOM = 30378 NFRAME= 1002 ISTART= 0 last = 1002 nstep = 1002 nfile = 1002 NSAVE = 1 NDEGF = 0 version 24 |======================== | 21%Error in readBin(trj, "numeric", size = 8, n = (a/8), endian = head$end) : invalid 'n' argument In addition: Warning message: In rbind(x, y, z) : number of columns of result is not a multiple of vector length (arg 3) inds <- atom.select(pdbfile, elety = "P") View(inds) inds

Call: atom.select.pdb(pdb = pdbfile, elety = "P")

Atom Indices#: 48 ($atom) XYZ Indices#: 144 ($xyz)

attr: atom, xyz, call

ca.inds <- atom.select(pdbfile, elety="CA") View(ca.inds) View(ca.inds) View(ca.inds) ca.inds

Call: atom.select.pdb(pdb = pdbfile, elety = "CA")

Atom Indices#: 94 ($atom) XYZ Indices#: 282 ($xyz)

attr: atom, xyz, call

casc.local.inds <- combine.select(ca.inds,inds, operator="+") Union of selects
Selected a total of: 142 atoms *

View(casc.local.inds) casc.local.inds[["atom"]] [1] 2 11 22 33 40 51 62 69 86 97 104 111 130 140 154 165 187 198 212 228 249 265 276 [24] 290 309 323 343 354 373 387 401 415 427 446 467 491 510 530 541 563 584 591 613 629 645 667 [47] 683 697 716 733 755 767 789 801 815 839 861 872 894 901 917 927 947 966 985 1005 1024 1036 1058 [70] 1070 1081 1091 1108 1122 1133 1147 1171 1181 1200 1214 1228 1250 1267 1286 1306 1313 1337 1353 1372 1394 1404 1415 [93] 1434 1444 1463 1496 1526 1556 1589 1622 1655 1689 1722 1753 1784 1817 1850 1881 1912 1945 1978 2009 2039 2069 2100 [116] 2130 2164 2194 2224 2255 2285 2316 2346 2379 2412 2445 2476 2510 2543 2576 2607 2637 2667 2697 2730 2763 2796 2826 [139] 2856 2889 2922 2952 xyz <- fit.xyz(pdbfile$xyz, mobile = dcdfile, fixed.inds = casc.local.inds$xyz, mobile.inds = casc.local.inds$xyz) Error in fit.xyz(pdbfile$xyz, mobile = dcdfile, fixed.inds = casc.local.inds$xyz, : input 'mobile' should be numeric how to solve this error > xyz <- fit.xyz(fixed = pdbfile$xyz, trtfile, fixed.inds = casc.local.inds$xyz, mobile.inds = casc.local.inds$xyz) Error in fit.xyz(fixed = pdbfile$xyz, trtfile, fixed.inds = casc.local.inds$xyz, : input 'mobile' should be numeric

Comments (2)