AMBER Archive (2009)

Subject: RE: [AMBER] Re: connect

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jun 15 2009 - 20:43:46 CDT

Hi Kirtana,

> I connected my residues in xleap and saved it as library file .When I
> save
> it as savepdb libraryfilename filename.pdb , and view the pdb file
> .This
> pdb file does not show any connectivity among the residues What can be
> the
> reason behind or I can proceed.
> I appreciate your help in this regard

As Bill correctly pointed out Leap does not add connectivity to the pdb file
hence other programs can only use bond by distance. Note you could try
saving as mol2. I think this will contain connectivity and a lot of programs
can read mol2. Alternatively if you use something like VMD you can first
load a prmtop file and then into this molecule load the pdb and VMD will use
the definitions in the prmtop file for drawing the bonds.

Good luck,
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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