[gmx-users] Re: the output of do_dssp
jiangsl at phys.sinica.edu.tw
Thu May 27 16:17:35 CEST 2010
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?
>> 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...
>> 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.
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