[gmx-users] OPLS force field issue....
swijesi at g.clemson.edu
Thu Dec 19 03:46:31 CET 2013
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?
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:
>> 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
>> 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 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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