[gmx-users] missing of methyl at N-terminal

Bhawana Gupta bhawana.gupta2010 at gmail.com
Fri Nov 7 05:10:16 CET 2008

hello everyone,

for doing peptide with usual amino acid simulation.
i m bringing my *.pdb file from insightII as i dont  know any other tool or
software from where i can get any pdb file (model peptide-Eg.
Ac-Ala-Ala-Ala-Ala-NHMe).But when i put my pdb file in gromacs by using
pdb2gmx. it give error that no C is present at 6 NH2 position.

tell me what to do.

either tell me the name of free software or tool from where i can get the
pdb of model peptide.
tell me one more thing that whether gromacs only take those pdb's which are
converted by babel????

Please help me out
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