VMD-L Mailing List

From: Leonardo G. Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Fri Jun 02 2006 - 13:22:41 CDT

On Fri, Jun 02, 2006 at 10:26:17PM +0530, Moumita Maiti wrote:
> Hi,
>
> I have attached the script ikx5.pgn which will generate 1kx5.psf and
> 1kx5.pdb file. It gives the errors for two DNA segments(DN0 and DN1) for
> example,
>
> "Warning: failed to set coordinate for atom O5* T:-72 DN0
> Warning: failed to set coordinate for atom C5* T:-72 DN0"
>
> Does this warning affect anyway in the ouput 1kx5.psf & 1kx5.pdb, what has
> been produced by this.

Yes it does. These atom names do not exist in CHARMM. If you include the
following aliases in your .pgn file, you should be go to go:

alias atom THY O5* O5'
alias atom THY C5* C5'
alias atom THY C4* C4'
alias atom THY O4* O4'
alias atom THY C1* C1'
alias atom THY C2* C2'
alias atom THY C3* C3'
alias atom THY O3* O3'
alias atom THY O2* O2'

alias atom GUA O5* O5'
alias atom GUA C5* C5'
alias atom GUA C4* C4'
alias atom GUA O4* O4'
alias atom GUA C1* C1'
alias atom GUA C2* C2'
alias atom GUA C3* C3'
alias atom GUA O3* O3'
alias atom GUA O2* O2'

alias atom ADE O5* O5'
alias atom ADE C5* C5'
alias atom ADE C4* C4'
alias atom ADE O4* O4'
alias atom ADE C1* C1'
alias atom ADE C2* C2'
alias atom ADE C3* C3'
alias atom ADE O3* O3'
alias atom ADE O2* O2'

alias atom CYT O5* O5'
alias atom CYT C5* C5'
alias atom CYT C4* C4'
alias atom CYT O4* O4'
alias atom CYT C1* C1'
alias atom CYT C2* C2'
alias atom CYT C3* C3'
alias atom CYT O3* O3'
alias atom CYT O2* O2'

Best,
Leo 

-- 
Leonardo Giantini Trabuco
Ph.D. candidate
Center for Biophysics and Computational Biology
University of Illinois at Urbana-Champaign