[gmx-users] capped residue

[Luciane V. Mello]

Dear all,

 I got an endcapped 15 residue-peptide. The carboxyl
 end-group is amidated: C(O)NH2 instead of C(O)OH.

the pdb file ends like:

ATOM    101  C   GLU    13      87.765  14.981  13.146  1.00  0.00     
1MOD 102
ATOM    102  O   GLU    13      86.689  15.414  12.738  1.00  0.00     
1MOD 103
ATOM    103  NT  NH2    14      88.017  14.621  14.438  1.00  0.00     
1MOD 104
HETATM  104  CA  CA     15      89.771  20.430   9.250  1.00  0.00     
1MOD 105
END

being CA a calcium ion.

When I try to run:

 pdb2gmx -f capped_fit.pdb

I got the following message:

Fatal error: Atom NT in residue NH2 15 not found in rtp database
             while sorting atoms


If I check at
/usr/local/share/gromacs/top/ffgmx.rtp

NT atom is there!

any idea?

thanks in advance,
Luciane



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