[gmx-users] missing of methyl at N-terminal
Mark.Abraham at anu.edu.au
Fri Nov 7 09:01:54 CET 2008
Bhawana Gupta wrote:
> 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.
Don't interpret error messages when reporting a problem with them to the
list. If your interpretation was good, then you probably wouldn't have
the problem. We'll be much more helpful if you give the actual input and
(relevant) output copied and pasted from your terminal window. I
shouldn't have to be guessing what actual problem means "it give error
that no C is present at 6 NH2 position".
In practice, InsightII uses PDB atom naming conventions that differ from
GROMACS ones. For small cases your best solution is to use it to
generate a PDB file, see what pdb2gmx doesn't like about it, refer to
the forcefield .rtp files (see chapter 5 of the manual) and fix them
with a text editor. If that becomes too tedious to be practical, invest
in writing some sed or Perl scripts to automate the conversion.
> either tell me the name of free software or tool from where i can get
> the pdb of model peptide.
Some options are given here
http://wiki.gromacs.org/index.php/Coordinate_File but the world seems to
be lacking a good, free solution.
> tell me one more thing that whether gromacs only take those pdb's which
> are converted by babel????
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