[gmx-users] lennard jones 6-12 value changing???

[라지브간디]

Dear Justin,


I have looked over the chapter 5 and had difficult to understand the interpreting the LJ 6-12 value for my ligand file.


I just want to give particular value only for NO ligand, therefore i want to know how do i give them in topology file? 


As you already mentioned that I should change them in [atomtypes] else special interaction in [nonbond_params] in ffnonboneded.itp file. If i do that, I wonder it could be giving this value for my protein too? 


What i want in here is, how do i specify the value only for NO ligand in .itp file which is created by pdb2gmx. I believe, the [pairs] column in the .itp also only for 1-4 LJ value?


Thanks in advance.






Dear gmx, 
> 
> I want set the particular value of lennard jones 6-12 for NO ligand for my simulation. I believe it has be mentioned in topology file created by force field. My questions is how to set these value in topology which created by CHARMM 27 ff? 
> 

The directives in ffnonbonded.itp control these interactions. You can either 
modify that file (or better, a local copy in case something goes wrong) or just 
add the relevant directives in your topology directly (new atom types in 
[atomtypes] or special interactions for existing atom types in 
[nonbond_params]). See Chapter 5 of the manual. 

-Justin