[gmx-users] amide-capped C-terminus; OPLS force field

[Justin Lemkul]

On 12/3/19 11:25 AM, Sahil Lall wrote:
> Hi,
>
>>> You need to add ions in the system to neautralise.
>>>
>>> and i think -0.18 qtotal considered as zero.
>> That is absolutely not the case. Rounding errors should never amount to 0.001 or even less.
> Thank you for clarifying that Justin, that is what I also thought too
>
>> If the OP is looking at charges in ffnonbonded.itp, those are never used and have no bearing on what should actually be defined in the topology.
>>
>> -Justin
>>
>> --
> But this leaves me with the original problem. Is there no way to have an
> amide C terminus and yet maintain neutrality of the system (with of
> course qtotal for everything else = 0 in the topology file)?

Of course there is. You just need to assign proper charges. Look at the 
NAC residue in the force field; this is exactly what you want as a terminus.

-Justin

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Justin A. Lemkul, Ph.D.
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