peptideBuilder

This is a plug-in for VMD (requires autopsf). The code allows building a peptide ab initio just from a sequence and the corresponding secondary structure or backbone internal coordinates. Add to the vmd path

lappend auto_path $YOURPATH

Example

Input for an ideal secondary structure (e.g. helical peptide): peptide.dat

h,ADFGEDT

Input for explicit torsion angles: peptide_full.dat

ALA -57 -47
GLU -57 -47
PHE -57 -47
GLY -57 -47

Running it in VMD:

package require peptideBuilder
::peptideBuilder::build_peptide peptide.dat ideal
::peptideBuilder::build_peptide peptide_full.dat full