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From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Tue Oct 13 2015 - 02:00:43 CDT
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If you have 8 rings, you’re going to need 8 chains (each with its own chain letter), and one segment per chain. If you write each chain to its own pdb file…
set all [atomselect top all]
set chains [lsort –unique [$all get chain]]
foreach chain $chains {
set towrite [atomselect top “chain $chain and protein”]
$towrite writepdb ${chain}.pdb
$towrite delete
}
$all delete
… then you can adjust your psfgen script:
package require psfgen
topology top_all36_prot.rtf
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
set chains {**** put your list of chains here ****}
foreach chain $chains {
segment $chain {first NONE
last NONE
pdb ${chain}.pdb
patch LINK ${chain}:14 ${chain}:1
patch LINK ${chain}:15 ${chain}:29
patch LINK ${chain}:29 ${chain}:43
coordpdb ${chain}.pdb
}
guesscoord
regenerate angles dihedrals
writepsf new.psf
writepdb new.pdb
… and unless I’ve made a typo somewhere or forgotten something, that should work.
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Nikhil Maroli
Sent: Tuesday, 13 October 2015 3:43 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Cyclic peptide nanotube psf second mail
Dear All,
This is my second mail regarding cyclic peptide nanotube psf, i run this script but i got only one ring in psf and new pdb i wanted to get for full tube
my system contains 8 rings in each rings 8 amino acids ,i able to make cyclic peptide
can anyone tell me how to make psf fir cyclic peptide nanotube
package require psfgen
topology top_all36_prot.rtf
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment A {first NONE
last NONE
pdb cpnl.pdb
}
patch LINK A:14 A:1
regenerate angles dihedrals
patch LINK A:15 A:29
regenerate angles dihedrals
patch LINK A:29 A:43
regenerate angles dihedrals
coordpdbcpn.pdb A
guesscoord
writepsf new.psf
writepdb new.pdb
thanks
--
Ragards,
Nikhil Maroli
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