From: Alexe Bojovschi (abojovschi_at_it.swin.edu.au)
Date: Wed Nov 02 2005 - 03:09:08 CST
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.
>******************************************************************
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