[gmx-users] amber ff gromacs

[virk]

Dear People,

I am trying to simulate glycine molecule using amber ff. I have changed the
residues in pdb file with N and C respectively.
ATOM      1  N    NGLY    1      -1.476   0.232   0.252  1.00  0.00
ATOM      2  CA  CGLY    1      -0.012   0.296   0.348  1.00  0.00
ATOM      3  C    CGLY    1       0.596  -0.652  -0.648  1.00  0.00
ATOM      4  O     GLY     1      -0.124  -1.320  -1.368  1.00  0.00
ATOM      5  OXT GLY     1       1.916  -0.760  -0.740  1.00  0.00
ATOM      6  H3   GLY     1      -1.736  -0.252  -0.592  1.00  0.00
ATOM      7  HA2 GLY     1       0.292   0.020   1.364  1.00  0.00
ATOM      8  HA1 GLY     1       0.320   1.320   0.132  1.00  0.00
ATOM      9  H    GLY     1      -1.636  -0.236   1.132  1.00  0.00
ATOM     10  H   GLY     1      -1.916   1.136   0.272  1.00  0.00
TER      11         GLY     1 
END 

But when I am using pdb2gmx, I am getting this error 
Residue 1 named NGLY of a molecule in the input file was mapped to an entry
in the topology database, but the atom CA used in that entry is not found in
the input file.

But atom CA is in the input pdb file and with same name in amber .rtp file
too. If I remove N and C prefixes in pdb file, pdb works for all other
fields.

I will be thankful for your help and time.

Kind Regards,
Amninder Virk
 

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