[gmx-users] Secondary structure not visible after convertingfrom .gro to .pdb

[bharat gupta]

Thanks Chris, I will check it.

What I suspect is that it could be due to multiple number of chains in my
protein. Do I need to treat this protein in a separate way during pdb2gmx
step ??


On Thu, May 29, 2014 at 10:42 AM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> I sometimes see this in VMD if the coordinates are truly awful (e.g, if
> the C-alpha atoms are way too far apart, then VMD does not recognize it as
> a proper backbone since no topology information is loaded and connectivity
> is inferred from distances). I also see this for some crystal structures
> (in VMD) and I am not sure exactly why, but I presume that something is not
> falling into an "accepted" region of conformational space to be recognized
> as a protein backbone. I presume the same is true for Pymol.
>
> Try to run a very small amount of MD and see if that improves things. It
> always does for me.
>
> Chris.
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of bharat
> gupta <bharat.85.monu at gmail.com>
> Sent: 28 May 2014 21:36
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Secondary structure not visible after
> convertingfrom .gro to .pdb
>
> I am not concerned about secondary structure changes. But I want to
> visualize the entire protein structure in ribbon form after energy
> minimization... When I see the converted structure (.gro to .pdb) in pymol,
> only one chain is visible. How can I see all the chains together
>
>
> On Thu, May 29, 2014 at 10:28 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >  [image: Boxbe] <https://www.boxbe.com/overview> This message is
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> >
> >
> > On 5/28/14, 9:24 PM, bharat gupta wrote:
> >
> >> Hi,
> >>
> >> I energy minimized a protein consisting 10 chains using gromacs. When I
> >> converted the structure of the protein from gro format to pdb format to
> >> visualize in Pymol, it shows only one chain in ribbon form and rest of
> the
> >> chains are not shown ... How to rectify this error ??
> >>
> >>
> > Visualization programs guess what secondary structure should be based on
> > the supplied geometry.  Sometimes they get it wrong.  If you're concerned
> > about secondary structure changes, you should be using a quantitative
> > method rather than visualization.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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>
> --
> Bharat
> Ph.D. Candidate
> Biomolecular Engineering Laboratory
> Pusan National University
> South Korea
> Mobile no. - 010-5108-3680
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