Re: PSF for CYCLIC PEPTIDE :

From: bay__gulf618_at_sina.com
Date: Sat Sep 26 2015 - 21:26:01 CDT

Hi Maroli,
I am the author of [JPCA 2010, 114, 2376], [JPCB 2010, 114, 12183] and have performed some modeling and simulations with cyclic peptide rings/nanotubes.

You can use the following commands, which would give a correct treatment for the terminal residues in the peptide rings.
segment U {pdb cpn.pdb; first none; last none; auto none }

I don't know the how the informations and how many atoms in you pdb file. I have writen a smart script to generate the correct pdb file for cyclic peptide rings from the peptide sequence. If the segment command above still don't work, I could send my script to you.

According [JACS 2003, 125, 2756], "the minimum ring (residue) number is given as n = 6, i.e., an even number of n = 6, 8, 10, 12,‚ÄČ... is available ... ". So I also wonder why do you use only 4 residues (U:4 U:1).

Ragards,
Jian Liu





bay__gulf618_at_sina.com
 
From: Nikhil Maroli
Date: 2015-09-26 19:15
To: vmd-l; namd-l
Subject: namd-l: PSF for CYCLIC PEPTIDE :

Dear All,
I wanted to do MD of cyclic peptide so for psf generation i done the following commands
package require psfgen
topology top_all27_prot_lipid.inp
segment U {
pdb cpn.pdb
auto none }
patch LINK U:4 U:1
coordpdb cpn.pdb U
regenerate angles dihedrals
guesscoord
writepdb cpn1.pdb
writepsf cpn1.psf

but end up in errors

(cpn) 8 % package require psfgen
topology top_all27_prot_lipid.inp
segment U {
pdb cpn.pdb
auto none }
patch LINK U:4 U:1
coordpdb cpn.pdb U
regenerate angles dihedrals
guesscoord
writepdb cpn1.pdb
writepsf cpn1.psf
1.6.2
>Main< (cpn) 9 % psfgen) reading topology file top_all27_prot_lipid.inp

psfgen) > CHARMM22 All-Hydrogen Topology File for Proteins and Lipids <<
psfgen) >>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<
psfgen) >>>>>>>>>>>>>>>>>>>>>> July 2004 <<<<<<<<<<<<<<<<<<<<<<<<<<
psfgen) All comments to ADM jr. via the CHARMM web site: www.charmm.org
psfgen) parameter set discussion forum
psfgen)
psfgen) Created by CHARMM version 31 1
psfgen) cross-term entries present in topology definitions
>Main< (cpn) 10 % psfgen) building segment U
psfgen) reading residues from pdb file cpn.pdb
psfgen) extracted 4 residues from pdb file
psfgen) disabling angle autogeneration
psfgen) disabling dihedral autogeneration
psfgen) Info: generating structure...psfgen) Info: skipping improper N-C-CA-HN at beginning of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
psfgen) Info: skipping bond C-N at end of segment.
psfgen) Info: skipping improper C-CA-N-O at end of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at end of segment.
psfgen) Info: skipping conformation CA-C-N-CA at end of segment.
psfgen) Info: skipping conformation N-CA-C-O at end of segment.
psfgen) Info: skipping conformation N-CA-C-N at end of segment.
segment complete.
>Main< (cpn) 11 % psfgen) applying patch LINK to 2 residues
psfgen) no atom O in residue LEU:4 of segment U
psfgen) Warning: add improper failed in patch LINK
psfgen) no atom HN in residue ALA:1 of segment U
psfgen) Warning: add improper failed in patch LINK
psfgen) no atom HN in residue ALA:1 of segment U
psfgen) Warning: add conformation failed in patch LINK
psfgen) no atom O in residue LEU:4 of segment U
psfgen) Warning: add conformation failed in patch LINK
>Main< (cpn) 12 % psfgen) reading coordinates from pdb file cpn.pdb for segment U
psfgen) Warning: failed to set coordinate for atom O LEU:4 U
>Main< (cpn) 13 % psfgen) regenerating all angles
psfgen) regenerating all dihedrals
>Main< (cpn) 14 % psfgen) Info: guessing coordinates for 36 atoms (2 non-hydrogen)
psfgen) Warning: failed to guess coordinate due to bad angle C N HT1
psfgen) Warning: failed to guess coordinate due to bad angle CB CA HA
psfgen) Warning: failed to guess coordinate due to bad angle CB CA HA
psfgen) Warning: failed to guess coordinate due to bad angle N C OT1
psfgen) Warning: poorly guessed coordinates for 6 atoms (2 non-hydrogen):
psfgen) Warning: poorly guessed coordinate for atom HT2 ALA:1 U
psfgen) Warning: poorly guessed coordinate for atom HT3 ALA:1 U
psfgen) Warning: poorly guessed coordinate for atom HA ALA:1 U
psfgen) Warning: poorly guessed coordinate for atom HA ALA:3 U
psfgen) Warning: poorly guessed coordinate for atom OT1 LEU:4 U
psfgen) Warning: poorly guessed coordinate for atom OT2 LEU:4 U
psfgen) Warning: failed to guess coordinates for 1 atoms
>Main< (cpn) 15 % psfgen) Info: writing pdb file cpn1.pdb
psfgen) Info: Atoms with guessed coordinates will have occupancy of 0.0.
psfgen) Info: pdb file complete.
>Main< (cpn) 16 % writepsf cpn1.psf
psfgen) Info: writing psf file cpn1.psf
psfgen) total of 61 atoms
psfgen) total of 61 bonds
psfgen) total of 118 angles
psfgen) total of 171 dihedrals
psfgen) total of 7 impropers
psfgen) total of 2 cross-terms
psfgen) Info: psf file complete.
>Main< (cpn) 17 %


and forming some extra atoms in the structure.
i hope someone can help me out here
--
Ragards,
Nikhil Maroli

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