[gmx-users] make_ndx for do_dssp

[Justin A. Lemkul]

Paymon Pirzadeh wrote:
> Justin,
> I produced the index file based on your suggestion, but when I ran the
> do_dssp, a completely different result was spit out comparing to what
> the whole protein analysis had given. Any ideas on why that might have
> happened?
> 

That depends on what "completely different" means.  I have no idea.  If you're 
only analyzing a subset of the residues, you're going to get a discontinuous 
plot that's probably going to look a whole lot different from any analysis done 
on the whole protein.  What's more, if you're only considering small fragments 
of the protein, then omitting surrounding residues from the analysis probably 
won't permit DSSP to find hydrogen bonding partners that are necessary to 
determine the correct secondary structure.

-Justin

> Paymon
> 
> On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote:
>> Paymon Pirzadeh wrote:
>>> Hello, I want to check the secondary structure of protein at particular
>>> residues. Since dssp needs all main chain atoms, does the following command
>>> at the make_ndx prompt makes the correct index file? 
>> You can answer that yourself by looking at the resulting index file.
>>
>>> 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45
>>>
>> To get these groups to merge, I think you probably need to do 5 & r 1 | ...
>>
>> -Justin
>>
>>> (Main chain atom of particular residues). regards,
>>>
>>> Paymon
>>>
>> -- 
>> ========================================
>>
>> 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
>>
>> ========================================
> 
> 

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

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

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