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

[Sidath Wijesinghe]

 Is g_x2top  the only way for my situation? or am i in the wrong track?

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?

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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-- 
Sidath Wijesinghe
Graduate Teaching Assistant
Dept Of Chemistry
Clemson University