[gmx-users] OPLS force field issue....

[Justin Lemkul]

On 12/18/13 9:46 PM, Sidath Wijesinghe wrote:
>   Is g_x2top  the only way for my situation? or am i in the wrong track?
>

There are numerous ways to generate topologies.  I have warned you that g_x2top 
is probably ill-suited for this task.  It works well for simple things.  It does 
not work well for complex systems.

> if i find the parameters for the missing parameters how can i get rid of
> sodium as u mentioned
> for the real system with Na+ ions?
>

I answered this question in my previous message.

-Justin

> Thank you!
>
>
> On Wed, Dec 18, 2013 at 9:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 12/18/13 9:32 PM, Sidath Wijesinghe wrote:
>>
>>> Justin,
>>>
>>> As i understood from reading and tutorial what i should do is, lets say i
>>> generated a topology file named as
>>> topol.top, so i need to add #include "oplsaa.ff/ions.itp" so it accounts
>>> for Na+.
>>>
>>> my question is..
>>>
>>> 1.how can i get rid of sodium? just removing the corresponding lines from
>>> the .pdb text?
>>>
>>
>> Yes, for the coordinate file processed by g_x2top.  Once the topology for
>> everything else is established and you have #included the topology for
>> sodium (as I explained before), you can use the original coordinate file.
>>
>>
>>   2. i tried with uncharged system for simplicity with less number of
>>> atoms..(
>>> here i replaced the COONa functional group with a CH3 group)
>>>
>>> but still g_x2top -f test.pdb -o np1.top -name np1 -ff oplsaa -pbc
>>>
>>> am getting this parameters missing..
>>>
>>> Can not find forcefield for atom C-147 with 1 bonds
>>> Can not find forcefield for atom C-148 with 1 bonds
>>> Can not find forcefield for atom C-873 with 1 bonds
>>> Can not find forcefield for atom C-874 with 1 bonds
>>> Can not find forcefield for atom C-939 with 1 bonds
>>> Can not find forcefield for atom C-940 with 1 bonds
>>> Can not find forcefield for atom C-1137 with 1 bonds
>>> Can not find forcefield for atom C-1138 with 1 bonds
>>> Can not find forcefield for atom C-1269 with 1 bonds
>>> Can not find forcefield for atom C-1270 with 1 bonds
>>>
>>> for that do i need to modify the atomname2type.n2t  the way i did
>>> earlier?or am i doing this wrong?
>>>
>>>
>> g_x2top is not very smart.  You have to give it all the information needed
>> for it to work.  Whenever you get this error, the solution is always the
>> same - those atoms are not accounted for by whatever is in the .n2t file,
>> so you need to add information to cover those atoms.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>
>> ==================================================
>>
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>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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