[gmx-users] MDsimulation of Protein-DNA complex

terrencesun at gmail.com terrencesun at gmail.com
Tue May 3 17:37:57 CEST 2016


What you have described is no physical. You should avoid doing that unless you have a better reason. In normal MD, counter ions don't need special treatment such as restraint to some solute.


> On 3 May 2016, at 9:51 PM, soumi <soumi90 at rediffmail.com> wrote:
> Dear All,&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; I am working on MDsimulation of Protein-DNA complex using AMBER99SB-ILDN force field with gromacs.In order to neutralize the net charge on the protein-DNA complex by adding the correct number of&nbsp; positive ions or negative ions&nbsp; I have used the following command in gromacs 
> gmx genion -s ions.tpr -o  solv_ions.gro -p topol.top -pname NA -nname CL -np 38
> When prompted, I choose group 13 &quot;SOL&quot; for embedding ions because I do not want to replace parts of protein-DNA complex with ions.In MM&nbsp; optimisation process for solvated complex,counter ions are easily separated from the solute .Such separated ions have no function as a counter ion.In order to avoid such situation I desire the positions of Na+ ions around DNA to be constrained within 5 A from the PO4- groups of DNA backbone,while the Na+ ions around protein were contrained within 6 A from the&nbsp; carbon atom of the carboxyl group of the negatively charged Asp 129 residue.How can the positions of Na+ ions around DNA be constrained within 5 A from the PO4- groups of DNA backbone by which command or method using&nbsp; gromacs exclusively (not AMBER TOOL /AMBER PACKAGE )?With Regards ,Soumi Das
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