[gmx-users] Ignoring H-atoms.

[Justin Lemkul]

On 2/7/17 3:42 AM, Amir Zeb wrote:
> Thanks Erik,
>
> I got the explanation you kindly posted regarding the posted discussion.
>
> I would like to extend the question that if some one does not flag the
> -ignh, so does it mean that the input H-atoms are still there and the force
> field will consider them during the rtp file generation?
> Further more, if the case is likely not to flag the -ignh, what might be
> the possible consequences?
>

The -ignh flag has one purpose, as Erik said, which is to ignore H atoms in the 
input coordinate file.  It does not necessarily have any relationship to any 
force field.  All force fields have their own conventions as to whether or not H 
atoms are represented (united-atom vs. all-atom, for instance) and how they're 
named (although this much is usually consistent).

The -ignh flag does one thing to potentially serve two purposes:

1. Avoid nomenclature inconsistencies.  Unfortunately, many programs use their 
own conventions for naming H atoms, which are often inconsistent with standard 
nomenclature.  Using -ignh gets rid of most problems instead of the user having 
to do find-and-replace throughout their file.

2. United-atom force fields.  An experimental or modeled structure with H will 
not be appropriate if you're using a UA force field (e.g. GROMOS), so ignoring 
the H will overcome errors that would arise about H atoms being found in the 
coordinate file that are not expected/needed.

-Justin

-- 
==================================================

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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