[gmx-users] adding ions in Gromacs 4.6.5
Justin Lemkul
jalemkul at vt.edu
Mon Nov 17 18:34:06 CET 2014
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
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