[gmx-users] any software which could convert a polypeptide sequence to a pdb file?

Itamar Kass itamar.kass at monash.edu
Wed Apr 20 06:55:45 CEST 2011


It seems like you look into modelling the polypeptide, if you have a 
good template you can use pymol ot even insight. If you wish to have an 
ab-initio model you can use sybyl or alike.

Good luck with it,

On 20/04/11 2:36 PM, Liao Chuan wrote:
> Dear gmx-users,
> I want to conduct simulations of a protein and its ligand, a 
> heptapeptide HXXXPAS, where X could be tyrosine, tryptophan, pheny 
> alanine, alanine. Thus, I will have to conduct a total number of 
> 4*4*4=64 runs. I've got the pdb file of the protein, but I have no 
> idea how to prepare the pdb files of those 64 heptapeptides with 
> sequences already known. Is there any software/script which could 
> convert a polypeptide sequence to a pdb file?  Any comment is appreciated!
> - Chuan


"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut

| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
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| Victoria 3800
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