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

[Sidath Wijesinghe]

could you please give me a hint about a suitable method for this task?

thank you!


On Wed, Dec 18, 2013 at 9:50 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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-- 
Sidath Wijesinghe
Graduate Teaching Assistant
Dept Of Chemistry
Clemson University