Hi Wu
Just load your trajectory on pdb file instead of amber parm.
Rahman
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*M*d* H*omaidur* R**ahman *( Research Scholar )
Lab No. 510, Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036, India
*Mobile No = +91- 7845991785*
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On Thu, Mar 30, 2017 at 5:53 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> TIP3P is a rigid water model - that bond is supposed to be there. When
> I want to get around this I just create separate representations for
> O-H1 and O-H2.
>
> -Dan
>
> On Thu, Mar 30, 2017 at 7:04 AM, 吴萌 <wumeng.shanghaitech.edu.cn> wrote:
> > Dear All,
> >
> > I am running a membrane protein MD simulation with Amber14. When load
> my trajectory in VMD(version 1.9.3), I found the display of water molecules
> is adnormal: there shown the third bonds between the two hydrogen atoms. I
> have tried diffrernt drawing method, but the problem is still there. Could
> it be my water model(tip3p I used) problem or the parameters? If so, how
> can I fix it.
> >
> > Any suggestions would be greatly appreciated.Thank you in advance!
> >
> > Sincerely,
> > Wu Meng
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Mar 30 2017 - 21:30:03 PDT
