[gmx-users] PRODRG warning

[Andrew Horsfield]

Hi Daan,

> One problem may be that your PDB file does not have proper atom names.
> How can GMX know which "C" is "C" if they are all called "C"? You
> might try it with C1 C2 C3 C4 etc. and see if that helps?

The PDB file I mailed to you goes only to PRODRG. The PDB file I fed to
Gromacs (based on the PRODRG output) was:

ATOM      1  HA  MYP            -6.108  30.035  20.765
ATOM      2  N1  MYP            -5.276  29.686  21.240
ATOM      3  C1  MYP            -4.110  30.463  21.020
ATOM      4  O1  MYP            -4.136  31.409  20.251
ATOM      5  C2  MYP            -2.973  29.975  21.825
ATOM      6  N2  MYP            -1.798  30.612  21.705
ATOM      7  C3  MYP            -0.802  30.158  22.460
ATOM      8  C4  MYP            -0.980  29.074  23.341
ATOM      9  N3  MYP            -2.132  28.426  23.469
ATOM     10  C5  MYP            -3.159  28.865  22.701
ATOM     11  N4  MYP            -4.343  28.184  22.814
ATOM     12  C6  MYP            -5.348  28.612  22.097
ATOM     13  N5  MYP            -6.571  28.005  22.221
ATOM     14  HC  MYP            -6.538  27.144  22.758
ATOM     15  HB  MYP            -7.191  27.989  21.417

Does PRODRG also need unique identifiers?

Cheers,

Andrew