[gmx-users] GROMOS atp file

[faride badalkhani]

Thanks a lot for your time and patience.

Truly yours,
Farideh


On Sat, Aug 15, 2015 at 6:24 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/15/15 9:51 AM, faride badalkhani wrote:
>
>> But all the nonbonded parameters for these Hydrogens are zero while they
>> are polar and they should be considered
>>
>>
> This is the convention of the force field.  Polar groups are dominated by
> electrostatics.  The van der Waals interactions are parametrized with the
> assumption that the H do not need LJ terms; the heavy atoms dominate the
> interaction.  This is just the way this particular force field works.  Look
> at the well depth and radii of HC - it's essentially non-existent, as well.
>
> -Justin
>
>
> On Sat, Aug 15, 2015 at 4:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 8/15/15 4:42 AM, faride badalkhani wrote:
>>>
>>> Dear all,
>>>>
>>>> I am having a question about Hydrogens in GROMOS FF. There are two
>>>> Hysrogens in .atp file of GROMOS FF as follows:
>>>>
>>>>      HC   1.00800 ;     hydrogen bound to carbon
>>>>         H   1.00800 ;     hydrogen not bound to carbon
>>>>
>>>> and all the nonbonded parameters for H are considered zero, but what
>>>> about
>>>> polar Hydrogens that are bounded to elements other than C (for example H
>>>> in
>>>> amino or amid groups)? How should I treat with these polar hydrogens?
>>>>
>>>>
>>>> That's what atom type H is - "hydrogen *not* bound to carbon."
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
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>>> University of Maryland, Baltimore
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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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> Gromacs Users mailing list
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