[gmx-users] pds files without bond information

Justin Lemkul jalemkul at vt.edu
Wed Feb 20 22:45:18 CET 2013

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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