VMD-L Mailing List

From: Leyla Celik (lc_at_chem.au.dk)
Date: Mon Mar 14 2005 - 04:13:13 CST

Hi,

I actually think i figured it out myself... It seems, that only C-terminal
residues does it, so it might be the psfgen-way to patch those.

/Leyla

Citat Ayse Meric OVACIK <movacik_at_ku.edu.tr>:

> check your topology file, there might be something wrong. which residue
> causes this error?
> Meriç
> Leyla Celik wrote:
>
> >Hi,
> >
> >I am trying to make psf and pdb files of my system when i encountered a
> warning
> >" failed to set coordinate for atom O". Psfgen creates the files, but when
> i
> >looked in them, instead of a backbone 'O', there was two 'OT' atoms bonded
> to
> >the carbonyl carbon (which is still 'C').
> >
> >Any suggestions on what to doo?
> >
> >Thanks,
> >Leyla
> >
> >
> >
> >
> >
>
> 

-- 
Leyla Celik
Kemisk Institut
Aarhus Universitet
Langelandsgade 140
8000 Århus C
Danmark
Tlf: +45 8942 3869
e-mail: lc_at_chem.au.dk