VMD-L Mailing List

From: Anurag Sethi (anurag.sethi_at_gmail.com)
Date: Mon Apr 07 2014 - 19:37:48 CDT

Hi Donald,

I suspect that either STAMP or VMD is not recognizing your modified residue
and the count of residues between multis and STAMP are getting messed up.
Could you send the modified structure?

-Anurag

Genius is nothing more or less than doing well what anybody can do badly. -
Amelia Barr

On Thu, Apr 3, 2014 at 11:33 AM, Donald Karr <donaldjkarr_at_gmail.com> wrote:

> Dear Users,
>
> I am trying to compare the structures of several aquaporins (1fqy, 1j4n,
> 1lda for reference) to a modified structure from the D chain of the 3d9s
> structure. The structures will align using Stamp but when I try to use Qres
> an error message appears.
>
> "An unknown error occurred while processing (residueIndex != num
> residueScores)"
>
> And then a bunch of stuff I do not understand. There is no QH score when
> highlighting the modified structure and another structure.
>
> The three aquaporins will align properly like they should but none of them
> will align with 3d9s proper resulting in the error message "Structures not
> aligned. Writing structure files could not be performed."
>
> I'm not sure where to go from here and am not sure if it is a problem with
> the structures or the system.
>
> Thanks for the help.
>