[gmx-users] alamethicin error

[pragya chohan]

i got this error "atom C not found in residue 84PHL while combining tdb and rtp" when i tried to do pdb2gmx
the commamd used is:
pdb2gmx -ter -ff gmx -f alamethicin.pdb -o alamethicin.gro -p ala.top
Select N-terminus type (start)
 0: NH3+
 1: NH2
 2: None
2
N-terminus: None
Select C-terminus type (end)
 0: COO-
 1: COOH
 2: None
1
C-terminus: COOH
even if i use option 0 i get an the same error. But if i ued option 2 in C-terminali get :
Atom C not found in residue 21 while adding improper... which is also PHL
84PHL is
ATOM    655  N   PHL    84      42.380  33.130  47.420  1.00  0.00
ATOM    656  H   PHL    84      41.620  33.340  46.800  1.00  0.00
ATOM    657  CA  PHL    84      43.050  34.310  47.980  1.00  0.00
ATOM    658  CB  PHL    84      43.960  34.910  46.910  1.00  0.00
ATOM    659  CG  PHL    84      45.060  33.960  46.410  1.00  0.00
ATOM    660  CD1 PHL    84      46.080  33.540  47.290  1.00  0.00
ATOM    661  HD1 PHL    84      46.090  33.860  48.320  1.00  0.00
ATOM    662  CD2 PHL    84      45.040  33.520  45.070  1.00  0.00
ATOM    663  HD2 PHL    84      44.280  33.880  44.390  1.00  0.00
ATOM    664  CE1 PHL    84      47.080  32.660  46.830  1.00  0.00
ATOM    665  HE1 PHL    84      47.870  32.330  47.480  1.00  0.00
ATOM    666  CE2 PHL    84      46.040  32.650  44.600  1.00  0.00
ATOM    667  HE2 PHL    84      46.050  32.350  43.570  1.00  0.00
ATOM    668  CZ  PHL    84      47.050  32.220  45.490  1.00  0.00
ATOM    669  HZ  PHL    84      47.830  31.570  45.140  1.00  0.00
ATOM    670  CX  PHL    84      41.990  35.310  48.450  1.00  0.00
ATOM    671  OY  PHL    84      40.950  34.570  49.110  1.00  0.00
ATOM    672  HY  PHL    84      40.110  35.090  49.220  1.00  0.00

pls help me
_________________________________________________________________
Windows Live Spaces is here! It’s easy to create your own personal Web site.
http://spaces.live.com/?mkt=en-in