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

[Justin Lemkul]

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

==================================================