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.