[gmx-users] Topology files

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 28 23:31:48 CET 2012

kirtana S wrote:
> Dear Users,
> In the gromacs manual on means to convert the pdb file to gromacs 
> topology file I need to use pdb2gmx. 
> Here I have to specify the force field .How to work with organic 
> residues which do not exists . 
> Since I had used general amber force field, and could not find this in 
> the /share/top/ directory . 
> Do I need to manually construct the .itp file for each residues. What 
> will be the easiest way to construct
> a solvated box with user defined residues in gromacs.

If the residue of interest will be a component of a polymeric molecule like a 
protein, refer to 
  If the molecule is a standalone species like a ligand, solvent, etc then all 
you have to do is #include an .itp file in the system topology.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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