AMBER Archive (2007)

Subject: Re: AMBER: problem related to visualizing of structure

From: deepti nayar (deepti.icgeb_at_gmail.com)
Date: Tue Apr 10 2007 - 04:18:38 CDT

thank you sir

I will use the recent version of vmd now. i was using vmd 1.8.5 right
now. do you think even this version would create problems?I am asking
this because if this is not the case, then i have to look into the
xleap built structure as according to me, there is nothing wrong with
th dipeptide

thanks

On 4/10/07, Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:
> Hi Deepti,
>
> which version of VMD are you using?? Did you try to load the .top and
> .crd files or only the .pdb file ?
>
> Old versions of VMD would add bonds based on a trivial distance
> criteria, so if you load a pdb file into an old VMD version, you will
> get some "strange" bonds , especially since the structure created with
> Leap is not a minimized structure ...
>
> My advice is to try to load into VMD the initial topology and coordinate
> files created by Leap instead of the pdb file. If the visualization will
> show you again strange bonds, then it is likely that something is wrong
> with your structure ....
>
> If I were you, I would also use VMD 1.8.6 - the latest VMD version ...
>
> Good luck
> vlad
>
>
>
> deepti nayar wrote:
>
> > hi
> >
> > I have made a dipeptide using xleap. my peptide is a non-standard
> > residue and so i saved the library first and then made the structure.i
> > have added suitable bonds and atoms as per my requirement. but when i
> > visualize it using vmd, i could see some unnecessary bondings there. i
> > was wondering if there is some mistake in the structure that i built
> > using xleap. its a phenylalanine-dehydrophenylalanine dipeptide.(i
> > have added the double bond between alpha carbon and beta carbon in
> > dehydrophenylalanine)
> >
> > i would be obliged if somebody tells me where is the problem
> >
> > thanks
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> --
> ----------------------------------------------------------------------------
> Dr. Vlad Cojocaru
>
> EML Research gGmbH
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
>
> Tel: ++49-6221-533266
> Fax: ++49-6221-533298
>
> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>
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