AMBER Archive (2004)

Subject: AMBER: unique atom names

From: anshul_at_imtech.res.in
Date: Wed Apr 07 2004 - 18:00:31 CDT

hi everyone,
when i load a pdb file in xleap some error is encountered because the atom
names are not unique.

 x = loadpdb NEWPDB.PDB Loading PDB file: ./NEWPDB.PDB -- residue 0:
duplicate [] atoms (total 38)
   ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
     (same-name atoms are reduced to a single atom) Unknown residue:
number: 0 type: Terminal/last ..relaxing end constraints to try for a
dbase match
  -no luck Creating new UNIT for residue: sequence: 0 Created a new atom
named: within residue: .R< 0>
  total atoms in file: 38
  The file contained 1 atoms not in residue templates

can any one tell me how to get the unique atom names in the pdb file.
following is apart of teh pdb file used here

ATOM 1 O11 mol 1 1.761 -4.471 0.000 -0.26836
ATOM 2 C10 mol 1 0.433 -4.717 -0.000 0.24255
ATOM 3 O12 mol 1 -0.034 -6.036 -0.000 -0.38298
ATOM 4 H24 mol 1 0.743 -6.666 0.000 0.28793
ATOM 5 C9 mol 1 -0.476 -3.652 -0.000 0.02250
ATOM 6 H22 mol 1 -1.051 -3.706 -0.816 0.04958
ATOM 7 H23 mol 1 -1.051 -3.706 0.816 0.04958
ATOM 8 C8 mol 1 0.274 -2.353 0.000 -0.01223
ATOM 9 H20 mol 1 0.849 -2.301 0.816 0.05023
ATOM 10 H21 mol 1 0.849 -2.301 -0.816 0.05023
ATOM 11 S7 mol 1 -0.700 -1.212 0.000 -0.15123
ATOM 12 C1 mol 1 0.000 0.000 0.000 -0.07300
ATOM 13 N6 mol 1 -0.675 1.169 0.000 0.11350
ATOM 14 N2 mol 1 1.350 0.000 0.000 0.11349
ATOM 15 C3 mol 1 2.025 1.169 -0.000 -0.14527
ATOM 16 N17 mol 1 3.425 1.169 0.000 0.05481
ATOM 17 C18 mol 1 3.926 -0.245 0.000 -0.07514
ATOM 18 C19 mol 1 5.426 -0.245 0.000 -0.08009
ATOM 19 H36 mol 1 5.760 0.226 -0.816 0.02689
ATOM 20 H37 mol 1 5.760 -1.187 0.000 0.02689
ATOM 21 H38 mol 1 5.760 0.226 0.816 0.02689
ATOM 22 H34 mol 1 3.593 -0.717 -0.816 0.02747
ATOM 23 H35 mol 1 3.593 -0.717 0.816 0.02747

any suggestion is greatly appreciated
with regards
anshul

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