Re: How to patch segments of aminoacids

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Nov 02 2005 - 10:35:19 CST

Hello,

Its probably best to break the two peptides into seperate segments.
Split the pdb file into two files.

you have segment A, just reference the first pdbfile

just add a build section for segment B and reference the second pdbfile.

when you add coordinates you also need to call the two pdb files
seperately.

Hope that helps
Brian

On Wed, 2 Nov 2005, Alexe Bojovschi wrote:

> Hi all
>
> Could somebody let me know how to patch two different segments (or only
> one) made up of few amino acids as not to get error message when I
> generate the psf file.
>
> Thank you for your support!
> Alex
>
> Simple case for two ALA aminoacids far away from each other (say 20A)
> when I generate psf I get a bond between the C from one ALA and the N
> from the other ALA of about 20Amstrons.
>
>
> First segment : (on of my cases :
> LEU-PHE-GLY-ALA-GLY-VAL-GLY-LYS-THR-VAL-LEU-ILE-MET-GLU
> and second segment (one of my cases:
> ASN-VAL-GLY-LEU-SER-VAL-SER-ARG-VAL-GLY-SER_ALA-GLY-THR
>
>
>
> ERROR MESSAGE:
>
> vmd -dispdev text -e chaine2.pgn
> Info) VMD for LINUX, version 1.8.2 (December 4, 2003)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 1 CPU detected.
> Plugin directory '/home/research/abojovschi/plugins/LINUX/molfile'
> does not exist!
> 1.3.3
> reading topology file top_all27_prot_na-likePDB.inp
>
> >>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
> >>>>>>> CHARMM22 Proteins and CHARMM27 Nucleic Acids <<<<<<<<<<
> from
> >>>> CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<<<
> >>>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<
> >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
> >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
> and
> \\\\ CHARMM27 All-Hydrogen Nucleic Acid Topology File ////
> \\\\\\\\\\\\\\\\\\ Developmental ////////////////////////
> Alexander D. MacKerell Jr. and Nicolas Foloppe
> August 1999
> All comments to ADM jr. email: alex,mmiris.ab.umd.edu
> telephone: 410-706-7442
>
> Created by CHARMM version 27 1
> ERROR! Explicit exclustions not supported, atom ignored.
> ERROR! FAILED TO RECOGNIZE LS
> duplicate residue key DUM will be ignored
> aliasing residue HIS to HSE
> aliasing residue ILE atom CD1 to CD
> building segment A
> reading residues from pdb file ATP-pocket-F-only-2-Chaines.pdb
> extracted 30 residues from pdb file
> Info: generating structure...
> Info: skipping improper N-C-CA-HN at beginning of segment.
> Info: skipping conformation C-N-CA-C at beginning of segment.
> Info: skipping conformation C-CA-N-HN at beginning of segment.
> Info: skipping bond C-N at end of segment.
> Info: skipping improper C-CA-N-O at end of segment.
> Info: skipping conformation CA-C-N-CA at end of segment.
> Info: skipping conformation N-CA-C-O at end of segment.
> Info: skipping conformation N-CA-C-N at end of segment.
> Info: segment complete.
> reading coordinates from pdb file ATP-pocket-F-only-2-Chaines.pdb for
> segment A
> Warning: failed to set coordinate for atom O THR:380 A
> Info: guessing coordinates for 219 atoms (2 non-hydrogen)
> Warning: poorly guessed coordinates for 5 atoms (2 non-hydrogen):
> Warning: poorly guessed coordinate for atom HT1 LEU:154 A
> Warning: poorly guessed coordinate for atom HT2 LEU:154 A
> Warning: poorly guessed coordinate for atom HT3 LEU:154 A
> Warning: poorly guessed coordinate for atom OT1 THR:380 A
> Warning: poorly guessed coordinate for atom OT2 THR:380 A
> Info: writing pdb file Chaine2.pdb
> Info: Atoms with guessed coordinates will have occupancy of 0.0.
> Info: pdb file complete.
> Info: writing psf file Chaine2.psf
> total of 421 atoms
> total of 421 bonds
> total of 762 angles
> total of 1087 dihedrals
> total of 69 impropers
> Info: psf file complete.
>
>
>
>
>
>
>
>
> >******************************************************************
> >* Alexe Bojovschi - PhD student
> >* Centre for Molecular Simulation
> >* Swinburne University of Technology
> >* P.O. Box 218 Hawthorn
> >* Victoria 3122 Australia
> >* Tel: +61 3 9214 4892
> >* Fax: +61 3 9214 5075
> >* http://www.it.swin.edu.au/centres/cms/
> >* Beauty in things lies in the mind which contemplates them.
> >******************************************************************
>

************************************************
  Brian Bennion, Ph.D.
  Bioscience Directorate
  Lawrence Livermore National Laboratory
  P.O. Box 808, L-448 bennion1_at_llnl.gov
  7000 East Avenue phone: (925) 422-5722
  Livermore, CA 94550 fax: (925) 424-6605
************************************************

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