[gmx-users] adding a new atom type

Justin Lemkul jalemkul at vt.edu
Wed Jul 25 13:50:09 CEST 2012

On 7/25/12 7:30 AM, Shima Arasteh wrote:
> Hi,
> The force field which I am using is CHARMM36.
> I added some new atom types to the atomtypes.atp .  Then I need to change the nonbonded.itp file. Are the atom names are used in .itp files? So how I find a last-defined atom types in the .itp file?

An "atom name" and an "atom type" are distinct concepts.  The atoms that are 
named in the topology must have atom types that are defined in ffnonbonded.itp. 
  Names are convenient labels and are irrelevant except for our own 
understanding of the content of our files; types define the nature of the 
interactions the atom experiences.  Parameters are assigned in the topology 
based on atom type.

> I just renamed some atomtypes and then added as the new atomtypes to .itp file, so I want to find a purposed atomtype and use its vdw parameter ( the same as what existed in .itp file.)

I'm not clear on the intent here.  You're creating duplicate atom types?  To 
what end?



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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