From: jonathan_at_ibt.unam.mx
Date: Wed Oct 25 2006 - 15:30:30 CDT
Hi. I used to run into the same problem with CHARMM, but the solution is really
stupid so it's worth trying with psfgen. Turns out that all I had to do was
adding two extra lines at the end of the PDB file. Thus, if your file ends with
something like
*************************************************
ATOM 999 O ASN A 17 13.737 -22.564 11.846 ...
ATOM 1000 OXT ASN A 17 14.445 -22.436 10.507 ...
*************************************************
try changing it to
*************************************************
ATOM 999 O ASN A 17 13.737 -22.564 11.846 ...
ATOM 1000 OXT ASN A 17 14.445 -22.436 10.507 ...
*************************************************
CHARMM was actually that picky. Maybe it will work for psfgen.
Regards,
J. Valencia
Quoting Vishal Kopardé <vnk_sim_at_yahoo.co.uk>:
> Hi All,
> During the making of the .psf file using psfgen I got these
> "warnings", what do they mean and whats their consequence:
> reading coordinates from pdb file frag7.pdb for segment I7
> Warning: failed to set coordinate for atom O ASN:21 I7
> Warning: failed to set coordinate for atom OXT ASN:21 I7
> I got these warnings consistently for the last two atoms in
> each protein fragment.
> Regards,
> Vishal
> p.s. complete psfgen output attached.
>
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