AMBER Archive (2005)

Subject: RE: AMBER: pdb file and xleap

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jul 19 2005 - 10:33:44 CDT

> 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 |

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