[gmx-users] Re: the output of do_dssp

[Mark Abraham]

----- Original Message -----
From: Hsin-Lin Chiang <jiangsl at phys.sinica.edu.tw>
Date: Thursday, May 27, 2010 0:28
Subject: [gmx-users] Re: the output of do_dssp
To: gmx-users at gromacs.org

> Hi, Justin:
> 
> I post my coordinate with protein translated by trjconv
> By this gro file, I get 0 structure and 13 coils.

Haven't you been saying for what seems like weeks now that you have 12 residues in your "protein"? If so...

<snip> 
> C   70   2.223   2.893   
> 1.484 -0.0883  0.1244 -0.1837
>     6ASN     O1   
> 71   2.111   2.941   1.505 -0.2557 
> -0.4837 -0.1041
>     6ASN     O2   
> 72   2.313   2.953   1.419 -
> 0.5561  0.0660  0.4455

Here, there's quite clearly an internal COO and NH3... hence it seems that you have two 6-residue chains. That's important data to be aware of, and to communicate to people who might help... Our belief that you really had a 12-residue peptide excludes this kind of issue from trouble-shooting, which ends up wasting everyone's time.

Mark

>     7LEU      
> N   73   1.111   2.804   
> 2.186  0.3062 -0.5955 -0.0550
>     7LEU     H1   
> 74   1.174   2.856   2.129  
> 0.2303 -0.3221  0.1077
>     7LEU     H2   
> 75   1.019   2.834   2.164  
> 0.0461 -1.9085 -0.8807
>     7LEU     H3   
> 76   1.126   2.815   2.284  
> 0.4122 -2.4532  0.1866
<snip>