[gmx-users] Using newly defined residue to neutralize the system

[Sajeewa Pemasinghe]

Thank you very much for the information.

On Wed, Jan 18, 2017 at 11:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/18/17 2:22 PM, Sajeewa Pemasinghe wrote:
>
>> So it should be monoatomic? Because this ion is a complex ion which has 19
>> atoms. So there would be no way of neutralizing with that kind of an ion
>> using genion I guess.
>>
>>
> Indeed, because genion is only intended for replacing water molecules with
> monoatomic ions.  You can, however, add your molecular ions (before adding
> water!) using gmx insert-molecules -ci -nmol.  Be sure to update the
> topology correctly.
>
> -Justin
>
>
> Best regards
>>
>> Sajeewa
>>
>> On Wed, Jan 18, 2017 at 9:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 1/18/17 3:04 AM, Sajeewa Pemasinghe wrote:
>>>
>>> Hi all,
>>>>
>>>> I have an itp file to a new residue MGH. It is an ion with a (+2)
>>>> charge.
>>>> I
>>>> have included the itp file in the topology file using #include MGH.itp.
>>>> My
>>>> question is, will I be able to use this MGH ion to neutralize my system
>>>> using "gmx genion" without any further modifications to the forcefield
>>>> files? If there are further modifications needed could you please tell
>>>> me
>>>> what they are?
>>>>
>>>>
>>>> gmx genion will a monoatomic ion of whatever name you choose (-pname)
>>> and
>>> whatever charge (-pq).  The name you give should match whatever is in
>>> MGH.itp.
>>>
>>> -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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> --
> ==================================================
>
> 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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