HI You:
This sounds like a bonding issue in branched oligosacharide's structures.
You should put TER cards at the appropriate locations in the PDB file. Then
u also need to include explicit bond commands in the tleap input. Note that
you only need bond commands for residues separated by a TER card.To check
for bonding issues, or to make sure your TER cards and bond commands are
right, open the top and crd files in vmd (use Amber 7 Parm and Amber 7
Restart as the file types).
Hope it helps
Sushil
On Fri, Aug 12, 2011 at 5:42 AM, Yun Shi <yunshi09.gmail.com> wrote:
> Hi All,
>
> Sorry for this lower-level question, but I searched the archive and still
> did not solve it.
>
> So I was trying to load a pdb file (only one oligosaccharide molecule)
> after
> source leaprc.GLYCAM_06, but what I got was
>
> ERROR: Comparing atoms
> .R<0hA 1>.A<C3 14>,
> .R<0hA 1>.A<C1 1>,
> .R<0hA 1>.A<H2 19>, and
> .R<0hA 1>.A<O2 20>
> to atoms
> .R<0hA 1>.A<C3 14>,
> .R<2hA 1>.A<C1 1>,
> .R<0hA 1>.A<H2 19>, and
> .R<0hA 1>.A<C1 1>
> This error may be due to faulty Connection atoms.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 140
> !FATAL: Message: Atom named C1 from 2hA did not match !
> !
> !ABORTING.
>
> So what it really means by "faulty Connection atoms"? I have already
> changed
> the sugar names according to GLYCAM naming convention.
>
> Any help is appreciated!
>
> Yun
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Received on Thu Aug 11 2011 - 22:00:03 PDT
