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
--
========================================
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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