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

Mark Abraham 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????

No idea.


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