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

라지브간디 rajiv at kaist.ac.kr
Wed Feb 27 18:25:08 CET 2013

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. 


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