[gmx-users] Re: gmx-users Digest, Vol 73, Issue 177

[Justin A. Lemkul]

Hsin-Lin Chiang wrote:
> Hi ,Mark:
> 
> I had announced my system is a dimer with each peptides have 6 residues.
> 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?
> 

It's not.  I already answered this:

http://lists.gromacs.org/pipermail/gmx-users/2010-May/051311.html

-Justin

> 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
>>
>>    

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================