i am loading a pdb file made in xleap.
thanks for the cooperation
On 4/10/07, Vlad Cojocaru <Vlad.Cojocaru.eml-r.villa-bosch.de> wrote:
> So, you didnt tell me whether you were trying to load a PDB file or a
> combination of toppology/coordinates files ?
> VMD 1.8.5 uses already a more complicated algorithm to assign bonds
> than the one in older VMD version ... so in principle your PDB should
> load fine in 1.8.5 ...
>
> But if you didnt do it yet, i would still try to check by loading a
> topology/coordinates combination into VMD and only if that produces the
> same result, I would definetely check the structure ...
>
> cheers
> vlad
>
> deepti nayar wrote:
>
> > 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.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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> >> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
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> >>
> >>
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> >> -----------------------------------------------------------------------
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> >> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
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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/
>
> ----------------------------------------------------------------------------
> EML Research gGmbH
> Amtgericht Mannheim / HRB 337446
> Managing Partner: Dr. h.c. Klaus Tschira
> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
> http://www.eml-r.org
> ----------------------------------------------------------------------------
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
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Received on Wed Apr 11 2007 - 06:07:36 PDT
