Tool : VMD
Sequence : VGQVVLGWKVSDLKSSTAVIPGYC
Building coordinate file without hydrogen :
mol new pep1.pdb
set s [atomselect top protein]
$s writepdb ubqp.pdb
Building PSF :
package require psfgen
topology top_all27_prot_lipid.inp
pdbalias residue ASP ASPP
pdbalias atom ILE CD1 CD
segment A {pdb pep1_q.pdb}
coordpdb pep1_q.pdb A
guesscoord
writepdb pep1_ptnd.pdb
writepsf pep1_ptnd.psf
Error : ASPP not recognized
ASPP contains required protonation state in topology (top_all27_prot_lipid.inp) file.
Please help.