[gmx-users] pdb for a structure with more then 300 atoms

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 3 13:26:43 CET 2007

nur avneet wrote:
> Dear all
> I have a peptoid sequence (peptoids have the amino acid side chain 
> appended to the amide nitrogen rather then alpha carbon) with more then 
> 300 atoms. Please guide me an easy way to generate its pdb or gromacs 
> coordinate and topology files, as PRODRG server doesnt work for more 
> then 300 atoms.

I doubt there is one, since you could be the first person to have a need 
for such a tool, and building them costs people time and resources.

For building the structure, you'll need to use structure-building 
software. There's lots of options out there, some better than others, 
but there's not a lot that's available for free that will suit your 
needs, I think. To get a topology, either build a library of peptoid 
residue topologies by analogy with peptides and then use the pdb2gmx 
machinery, or try giving PRODRG a set of fragments and glue them 
together by hand.

Otherwise, I feel I should re-iterate Tsjerk's sentiments from November 
  about doing peptoid simulations "Don't. Don't even think of going 
there, without understanding molecular simulations of 'ordinary' 
biological systems, both in terms of theory and practice." The fact that 
you're needing to ask these questions suggests to me that the problem 
you have is not one that you have the resources to tackle at this point 
in time.


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