AMBER Archive (2005)

Subject: RE: AMBER: pdb file and xleap

From: Wai Keat Yam (yamwaikeat_at_yahoo.com)
Date: Thu Jul 21 2005 - 01:01:07 CDT

Dear Ross,

Thanks for your suggestion, it works perfectly. Thanks
a lot.

keat

--- Ross Walker <ross_at_rosswalker.co.uk> wrote:

> > I have ran a few minimizations using sander for a
> very
> > large biomolecule with many bad contacts. After
> the
> > second minimization, I decided to check my
> structure
> > before proceeding further minimization. I used the
> > "ambpdb" command to create pdb file from the rst
> file
> > and its prmtop file as well.
> >
> > When I tried to view the pdb file (that were
> created
> > using ambpdb) using viewer (VMD, insightII), I
> found
> > that the structure has a lot of broken bonds. Then
> > when I view it again in xleap, the structure looks
> ok
> > without any broken bonds like the one I saw in
> > viewers.
> >
> > So, which one should I trust? the viewer? or
> xleap??
> > anyone can help to explain this? should I proceed
> > further minimization?
>
> When viewing pdb's in VMD it bonds atoms based on
> distance and so if atoms
> are too far apart they will be drawn as if unbonded.
> This is typical if you
> have a bad system as in your case. If you want to
> see the actually bonding
> topology that sander will use you need to use the
> prmtop file. You can open
> VMD, load the prmtop file as a new molecule and then
> into that molecule
> either load the pdb file or the restrt file from the
> minimisation. In this
> approach all the atoms will be bonded using the
> bonding information in the
> prmtop file.
>
> Beware that the lack of bonds when just loading the
> pdb file suggests that
> your structure still has problems so be careful if
> you start MD on this
> structure.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel: +1 858 784 8889 | EMail:-
> ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on
> request |
>
> Note: Electronic Mail is not secure, has no
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>
>
>
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Wai Keat, Yam (Ms.)Molecular Simulation & Computation Group (MSC)Laboratory of Biocrystallography & Structural Bioinformatics (Makmal Biokristalografi & Bioinformatik Struktur),University Science Malaysia, Minden, 11800 Pulau Pinang,Malaysia.Tel: 604-6533888 ext. 2437

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