[gmx-users] Re: the output of do_dssp

[Hsin-Lin Chiang]

Hi ,Mark:

I had announced that my system is a dimer with each peptides have 6 
residues in my first post.
I'm sorry if I didn't express it  to be understood easily.
Can you please tell me why 13 coils are reasonable if my systems is a dimer?

regards,
Hsin-Lin
>> 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
>
>