[gmx-users] adding ions in Gromacs 4.6.5

[Justin Lemkul]

On 11/17/14 6:42 AM, soumadwip ghosh wrote:
> Dear all,
>                I am currently working on  double stranded DNA aggregation
> and I require to add tetramethyl ammonium ions in my system. I know there
> are certain files to be modified in the force field directory for this
> purpose but I dont know which files. I am using Gromacs 4.6.5 and Charmm 27
> forcefield. I created the following pdb file using Gauss view 5.0.8. I will
> be highly obliged if someone tells me how and which files are to be
> modified to run the simulations in presence of this ion,
>

You don't need to modify force field files to simulate this species, you just 
need to generate a topology (.itp) for it.  You only need to modify the force 
field if you're adding a new building block for pdb2gmx or if you need to add 
new atom types (which for tetramethylammonium in CHARMM you should not have to).

-Justin

>
>
> TITLE       Required
> REMARK   1 File created by GaussView 5.0.8
> HETATM    1  N           0       3.666  -1.350  -1.577
>    N
> HETATM    2  C           0       4.157  -0.657  -2.777
>    C
> HETATM    3  H           0       5.227  -0.657  -2.777
>    H
> HETATM    4  H           0       3.800  -1.161  -3.651
>    H
> HETATM    5  H           0       3.800   0.352  -2.777
>    H
> HETATM    6  C           0       4.156  -0.657  -0.377
>    C
> HETATM    7  H           0       3.800   0.352  -0.377
>    H
> HETATM    8  H           0       3.800  -1.161   0.497
>    H
> HETATM    9  H           0       5.226  -0.657  -0.377
>    H
> HETATM   10  C           0       4.156  -2.736  -1.577
>    C
> HETATM   11  H           0       3.800  -3.240  -2.451
>    H
> HETATM   12  H           0       5.226  -2.736  -1.577
>    H
> HETATM   13  H           0       3.799  -3.240  -0.703
>    H
> HETATM   14  C           0       2.196  -1.350  -1.577
>    C
> HETATM   15  H           0       1.840  -0.341  -1.577
>    H
> HETATM   16  H           0       1.840  -1.854  -2.451
>    H
> HETATM   17  H           0       1.840  -1.854  -0.703
>    H
> END
> CONECT    1    2    6   10   14
> CONECT    2    1    3    4    5
> CONECT    3    2
> CONECT    4    2
> CONECT    5    2
> CONECT    6    1    7    8    9
> CONECT    7    6
> CONECT    8    6
> CONECT    9    6
> CONECT   10    1   11   12   13
> CONECT   11   10
> CONECT   12   10
> CONECT   13   10
> CONECT   14    1   15   16   17
> CONECT   15   14
> CONECT   16   14
> CONECT   17   14
>
> Thanks in advance
> Soumadwip Ghosh
> Senior research fellow,
> Indian institute Of Technology, Bombay,
> India
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================