[gmx-users] charge distribution

[Justin Lemkul]

On 12/27/14 3:54 PM, elham tazikeh wrote:
> Dear gromacs users
> i d like to know about charge distribution in .itp file that how can fix
> the charge of atoms
> for instance, i simulated Aspirin in Human serum albumin, and i want to
> know about their charges
> in an article charge distribution was as below, but in my .itp file
> (aquired by PRODRG server) i had 11 atoms instead of 13 atoms

Neither is enough atoms for aspirin, which should have 17 atoms in its 
united-atom representation (explicit H on aromatic C).  Aspirin would have 13 
atoms if the aromatic H are not explicit (wrong for Gromos96).

-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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