"If" statement parameters

Dear all,

I am working with a protein system that involves some pi-cation and pi-pi interactions with Arg, Lys, His, and Tyr on the amber and charm forcefields. I am wondering if it is ok to have custom parameters for these groups only IF they are next to each other.

I don’t understand what you are asking for. You can not have custom parameters based on spatial proximity. You can set custom parameters for specific atom pairs by giving atoms specific atom types and setting the parameters for those types.

Oh yes. That is what I am asking for. I am now adding some special interaction terms via [ nonbond_params ]. My only question is what is the difference between setting the epsilon and sigma values using nonbond_params and pairtypes and which one should be tinkered with. For example, I want to increase the interaction strength between the guanidinium group of ARG and a tyrosine (to mimic better pi-cation interactions).

[nonbond_params] override LJ combination rules for all pairs of the listed atom types. [pairtypes] are for 1-4 interactions. You want to modify the former, not the latter.

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