From: Victor (ovchinnv_at_gmx.com)
Date: Sun Aug 25 2013 - 11:28:45 CDT
Rasti,
If you look at what the patch actually does:
http://code.google.com/p/charmming/source/browse/trunk/head/charmming-private/toppar/top_all22_prot.rtf#1577
you might try "link U:5 U:1" instead. After you do this, open the psf
and see if there is a bond that corresponds to the link you are trying
to create (should be a pair of corresponding atom indices in the BONDS
section, hopefully at the end of it).
--Victor
On 08/25/2013 08:54 AM, rasti wrote:
>
> 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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