[gmx-users] Query regarding do_dssp program

[Justin Lemkul]

On 1/15/20 12:27 AM, Sundari wrote:
> I tried all the options.. I load gro file instead of xtc. At zero frame I
> gave representations new cartoon + secondary structure.. then I calculate
> sec str details by going on vmd timeline.
> I don't know what I am missing.. I am doing the same which I used all the
> time.
> Because these are two totally different secondary structures that's why I
> was worrying.. because these are major structures one reports so Very
> important to resolve this issue.

Without access to the coordinate file, there's nothing I can tell you. 
If you want to send me that snapshot off-list, I can probably take a 
quick look and see if I can get to the bottom of it.

-Justin

> On Wednesday, January 15, 2020, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 1/13/20 9:15 AM, Sundari wrote:
>>
>>> Yes, Sir,  I  made the gro file for a particular time by using "gmx
>>> trjconv" command ( also checked with -pbc mol, whole, no_jump options )
>>> but every time the 2ndary structure visualization in vmd is different from
>>> dssp sequence of residues in gromacs. Fox example in my protein dssp shows
>>> 8 residues making beta-sheets but when I load that particular time frame
>>> in
>>> vmd for visualizing the structure,  these 8 residues showing 5-helix
>>> structure.
>>>
>>> Please suggest something.
>>>
>> I'm afraid I can't. Those are two completely different hydrogen bonding
>> patterns and I can't imagine how the algorithms would differ so
>> dramatically. I have seen VMD render coils for helices and sheets but never
>> a totally different secondary structure. Be sure you're telling VMD to
>> re-compute structures and re-color the secondary structure elements at
>> every snapshot for trajectory visualization, otherwise it will render
>> everything the same as the initial frame, which will obviously be wrong in
>> the case of large structural changes.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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