[gmx-users] Partial charges calculation

Justin Lemkul jalemkul at vt.edu
Thu May 17 14:13:48 CEST 2018

On 5/17/18 6:36 AM, rose rahmani wrote:
> Hi,
> I want to calculate partial charges for nanotube capped with amino acid. I
> use DFT calculation when it is just nano tube with out any amino acid. As
> far as i know the amino acid partial charges for AA in amber99 are
> calculated by
> HF/6-31G* RESP calculation.
> The question is that, if i use DFT calculation for optimizing and
> calculating partial charges for nanotube- amino acid system, would amino
> acid partial charges be wrong or overstimated? I want to use this
> structures an an input(.itp file) for MD simulations in GROMACS  using
> amber99 ff.

Force field parameters must be derived in the same way. That means using 
the same QM model chemistry and any other applicable settings. Force 
fields have to be balanced; if they're not, all you've got is a random 
number generator.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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