[gmx-users] charge assign acetaminophen

[Justin Lemkul]

On 6/29/16 3:54 AM, elham tazikeh wrote:
> Dear GMX users;
> would you please help me about assigning the charges of my ligand
> (acetaminophen) for entrance to simulation
> i'd like to use the groups in aminoacids.rtp file in my force field
> (gromos53a6) but i don't know how extract my charges

This begins with an understanding of how the force field works and what 
literature has been published on it to date.  Unfortunately, GROMOS96 is highly 
empirical, with few (if any) details of QM charge calculations available in the 
published literature.  Initial guess charges historically come from DFT to match 
the ESP of a given molecule, and then are empirically refined against 
condensed-phase properties.  The subsequent adjustment is indeed highly 
empirical and somewhat frustrating if you don't have experience and solid 
chemical intuition.  But overall, as with most additive force fields, you can 
piece together the molecule from building blocks (in this case, a carboxylate, 
phenyl ring, and N-methyl acetamide).  But the problem is in validating that 
topology; you need some target data to confirm that the approach was right. 
You'll likely also need to do some dihedral refinement on the N-methyl acetamide 
linkage to the phenyl ring since AFAIK no analog exists in the force field and 
those torsions will be rather rigid due to conjugation.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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