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

[Sidath Wijesinghe]

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?
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
>>  UNK
>> > ATOM   7884 SOD  UNK     1     40.1388 -263.52 64.6776  1.00  0.00
>>  UNK
>> > ATOM   7885 SOD  UNK     1     18.3684 -236.89 77.4756  1.00  0.00
>>  UNK
>> > ATOM   7886 SOD  UNK     1     14.5668 -246.09 79.7592  1.00  0.00
>>  UNK
>> > ATOM   7887 SOD  UNK     1     15.7704 -239.23   76.65  1.00  0.00
>>  UNK
>> > ATOM   7888 SOD  UNK     1     14.7888 -242.75 78.6228  1.00  0.00
>>  UNK
>> >
>> > 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
>> the
>> > 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
>> to
>> 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
>> "normal"
>> 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
>> with
>> 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
>>
>> --
>>
>> ==========================================
>>
>> 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
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>
> --
> Sidath Wijesinghe
> Graduate Teaching Assistant
> Dept Of Chemistry
> Clemson University
>
>


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