[gmx-users] Query regarding do_dssp program

[Sundari]

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.

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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>