From: rasti (rasti_at_ut.ac.ir)
Date: Sun Aug 25 2013 - 07:54:50 CDT
Dear NAMD users,
iam trying to build psf file for a cyclic peptide
and i keep facing following problem:
1) when i use the pdb relates to
the cyclic form peptide (generated by hyperchem), VMD ignores the cyclic
structure and remove the bond between first and last residues adding
extra O and N instead.
package require psfgen
psfcontext reset
topology top_all27_prot_lipid_modified.rtf
pdbalias atom ILE CD1CD
pdbalias residue HIS HSE
segment U {pdb peptide.pdb}
coordpdb
peptide.pdb U
guesscoord
writepsf cyclic.psf
writepdb cyclic.pdb
2)
when i use the pdb relates to the linear form together with patch
LINK command to link first and last residues and build circular peptide,
it keeps failing again. The report says " applying patch LINK to two
residues ", but there is no visual of the circularity when i open pdb by
VMD.
package require psfgen
psfcontext reset
topology
top_all27_prot_lipid_modified.rtf
pdbalias atom ILE CD1 CD
pdbalias
residue HIS HSE
segment U {
first NONE
last NONE
pdb peptide.pdb
}
patch
LINK U:1 U:5
regenerate angles dihedrals
coordpdb peptide.pdb
U
guesscoord
writepsf cyclic.psf
writepdb cyclic.pdb
Any help will
be
extremely appreciated,
Behnam
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