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