Re: [AMBER] problem in .pdb after md simulation

From: Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
Date: Tue, 16 Jun 2015 09:54:25 +0200

I am not seeing any problem in visualising your PDB in either VMD or
Chimera. Images attached herewith. 1st one is the representation generated
by Chimera and second one is that of VMD. May be if you are opening in VMD
you might try changing the representation and select new cartoon.

On Tue, Jun 16, 2015 at 9:52 AM, Soong Jiaxin <jiaxinsoong.gmail.com> wrote:

> It looks fine to me in VMD. I don't understand what you meant. Perhaps you
> can try to change the graphical representation?
>
> On 16 June 2015 at 15:34, Vishal Nemaysh <vishal.bioinfotech.gmail.com>
> wrote:
>
> > Oh i m sorry madam...
> >
> > On Tue, Jun 16, 2015 at 1:04 PM, Vishal Nemaysh <
> > vishal.bioinfotech.gmail.com> wrote:
> >
> > > Sir i mean when u see my pdb structure which i attached in my mail u
> can
> > > batter understand..
> > > plz suggest my how can i resolve this
> > >
> > > On Tue, Jun 16, 2015 at 12:25 PM, Soong Jiaxin <jiaxinsoong.gmail.com>
> > > wrote:
> > >
> > >> May I know what do you mean by "bunches of sticks"? Did you visualise
> it
> > >> in
> > >> VMD?
> > >>
> > >> On 16 June 2015 at 14:52, Vishal Nemaysh <
> vishal.bioinfotech.gmail.com>
> > >> wrote:
> > >>
> > >> > Hi,
> > >> > i have simulate my protein in 10ns. but after that the structure
> > >> geometry
> > >> > is looking somewhat like bunches of sticks in .pdb structure is
> appear
> > >> ..
> > >> > please suggest me how to resolve this..
> > >> > the .PDB file is attached here with..
> > >> >
> > >> > thanking you,
> > >> >
> > >> >
> > >> > --
> > >> > Vishal
> > >> > Research Scholar,
> > >> > Neuropharmaceutical Chemistry lab.,
> > >> > Dr. B. R. Ambedkar Center for Biomedical Research,
> > >> > University of Delhi, Delhi-110007
> > >> > Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com
> >*
> > >> > Phone: 91-11-27662778 Mobile: 91+9650736653
> > >> >
> > >> > _______________________________________________
> > >> > AMBER mailing list
> > >> > AMBER.ambermd.org
> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >
> > >> >
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > >
> > > --
> > > Vishal
> > > Research Scholar,
> > > Neuropharmaceutical Chemistry lab.,
> > > Dr. B. R. Ambedkar Center for Biomedical Research,
> > > University of Delhi, Delhi-110007
> > > Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
> > > Phone: 91-11-27662778 Mobile: 91+9650736653
> > >
> >
> >
> >
> > --
> > Vishal
> > Research Scholar,
> > Neuropharmaceutical Chemistry lab.,
> > Dr. B. R. Ambedkar Center for Biomedical Research,
> > University of Delhi, Delhi-110007
> > Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
> > Phone: 91-11-27662778 Mobile: 91+9650736653
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Thanks & Regards;
Soumendranath Bhakat
Research Assistant, Division of Biophysical Chemistry, CMPS, Lund
University, Sweden
Homepgae: https://cbiores.wordpress.com/
ResearchGate: https://www.researchgate.net/profile/Soumendranath_Bhakat2
Google Scholar: http://scholar.google.com/citations?user=Q1_nDMcAAAAJ&hl=en
Past: Molecular Modelling and Drug Design Research Group
Discipline of Pharmaceutical Sciences
UKZN, Westville
Weblink: http://soliman.ukzn.ac.za/Home.aspx
and Department of Pharmaceutical Sciences
Birla Institute of Technology, Mesra, India
in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/



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chimera_image.png
(image/png attachment: chimera_image.png)

Received on Tue Jun 16 2015 - 01:00:05 PDT
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