[gmx-users] alamethicin error

[Mark Abraham]

pragya chohan wrote:
> 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

There's a warning given by pdb2gmx about this forcefield. You would do 
well to read it.

> 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

So, what important part of an amino *acid* residue is missing from this 
fragment?

Mark