[gmx-users] pds files without bond information

[Justin Lemkul]

On 2/20/13 1:59 PM, cdo wrote:
> Hi all,
>
> I'm new to Gromacs with a very basic question while I was reading tutorials.
> Tried to search this but I couldn't narrow down to useful discussions so
> far.
>
> It's simple. I saw some pdb files in the Tutorias. (such as LYSOZYME). But
> this particular pdb file do not have all the connectivity information. But
> still seems to work well in creating topology files. How is this possible?
>
> Don't I have to have all the connectivity information correctly in pdb file
> to start with?  What is the minimum requirement for the pdb file to be used
> in Gromacs?
>

One does not even need a .pdb file, strictly speaking.  Gromacs deals with many 
file formats, though .pdb files are quite common.  Other formats (.gro, .g96, 
etc) don't even have the option to include bonded information.

> Does pdb2gmx generate bondtype and atom type information correctly even
> without some connectivity information in the pdb file?    How complete
> information about the structure of molecules should I have in order to
> correctly generate input files for Gromacs?
>

Connectivity is defined in the .rtp file(s) for your chosen force field.  Bonds 
are determined based on atom names.  The assumption is that the starting 
geometry is reasonable.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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