[gmx-users] OPLS force field issue....
swijesi at g.clemson.edu
Thu Dec 19 03:32:21 CET 2013
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
my question is..
1.how can i get rid of sodium? just removing the corresponding lines from
the .pdb text?
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?
On Tue, Dec 17, 2013 at 10:49 AM, Sidath Wijesinghe
<swijesi at g.clemson.edu>wrote:
> Thank you very much!
> On Tue, Dec 17, 2013 at 10:25 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On Tue, Dec 17, 2013 at 10:09 AM, Sidath Wijesinghe
>> <swijesi at g.clemson.edu>wrote:
>> > Justin,
>> > so that means delete these lines "
>> > ATOM 7882 SOD UNK 1 42.69 -261.86 64.056 1.00 0.00
>> > UNK
>> > ATOM 7883 SOD UNK 1 39.09 -260.89 62.8968 1.00 0.00
>> > ATOM 7884 SOD UNK 1 40.1388 -263.52 64.6776 1.00 0.00
>> > ATOM 7885 SOD UNK 1 18.3684 -236.89 77.4756 1.00 0.00
>> > ATOM 7886 SOD UNK 1 14.5668 -246.09 79.7592 1.00 0.00
>> > ATOM 7887 SOD UNK 1 15.7704 -239.23 76.65 1.00 0.00
>> > ATOM 7888 SOD UNK 1 14.7888 -242.75 78.6228 1.00 0.00
>> > i have total of 48 sodium atoms...
>> > correspond to all the sodium atoms in test.pdb file and let it run with
>> > g_X2top?
>> > i am not clear about what u meant here...
>> > "Then modify
>> > the [molecules] directive to reflect the sodium ions and proceed with
>> > intact coordinate file"
>> I'm suggesting you simplify what you are doing to try to give g_x2top a
>> break. It is not very adept at doing what you are trying to make it do.
>> You have sodium ions. They're not bonded to anything. They don't need
>> be considered as one "molecule" along with the rest of the system.
>> Therefore, you don't need g_x2top to do anything with them. In a
>> Gromacs workflow, one takes a solute, gets a topology, adds some solvent
>> (using the #include mechanism for solvent, not generating a whole new
>> topology), then maybe adds some ions or other small molecules (again
>> #including a pre-existing topology) and the system is built. Now
>> reverse-engineer that. If you have some small species like ions, why
>> reinvent the wheel? You already have their topology in ions.itp, so you
>> just #include that in your final system topology and write the entry in
>> [molecules] yourself.
>> If that's still confusing, please spend some time with tutorials (my own
>> lysozyme tutorial walks you through topology organization and how Gromacs
>> normally functions) and the manual, specifically Chapter 5. Then, once
>> you're comfortable with the file hierarchy and such, dive into g_x2top
>> something simple, like one of your molecules, and make sure you know
>> exactly what's going on. Then add more layers of complexity until you get
>> the result you need or the program breaks completely ;)
>> 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
Graduate Teaching Assistant
Dept Of Chemistry
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