[gmx-users] GROMOS atp file

faride badalkhani farideh.khamseh at gmail.com
Sat Aug 15 15:51:53 CEST 2015


But all the nonbonded parameters for these Hydrogens are zero while they
are polar and they should be considered

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
>
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> Justin A. Lemkul, Ph.D.
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