[gmx-users] The .pdb file compatible with structure of .itp file,

Justin Lemkul jalemkul at vt.edu
Thu Sep 6 20:56:07 CEST 2012

On 9/6/12 2:43 PM, Ali Alizadeh wrote:
> Dear All users
> I want to make a .pdb file that's compatible with structure of .itp file.
> Is it possible?
> Because of in some cases that .pdb file is not compatible with .itp file,I
> cannot  add new molecules to force fields.
> what software does this work?

The contents of a coordinate file (any format) and a topology must be the same 
in terms of the number of atoms, their order, and their names.  Topologies can 
be made from coordinate files (using pdb2gmx), but coordinate files cannot be 
made from topologies.  There are various programs capable of creating coordinate 
files, but there is no guarantee that they match an existing .itp file.  Any 
corrections (atom names, atom order) usually have to be made in a text editor.



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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