Hi, in theory you must to modify the leaprc file located in $AMBERHOME/dat/leap/cmd/... and cross one's fingers

I never see this kind of operations, but why you need to use two forcefields for the same kind of molecule? I mean they are both proteins and the ildn forcefield introduce minimal modifications to the ff99sb ff...tried to use any of both forcefields to the entire system?

Hi Diego,

I am working with proteins only but both have different properties one is structured and another is unstructured (Intrinsically disordered protein). Both shows different structural properties, hence looking for integrating two different force fields.

Thank you for your answer

Hi Naga!

Of course both proteins have very different properties but my point is why use different force fields for each protein? what makes you think they're going to reproduce better the properties of each protein with differents (but not too much) forcefields?

The forcefields reproduce "well" some properties of native structured proteins but Im not so sure that could work well with ID proteins...but this is not a reason to not simulate the system. You will need a lot of experimental data to "ask something" to the simulations. We follow the discussion!

Hi Naga,

I am curious. How do you plan to deal with the interaction between the two proteins? In my study of association between an ordered protein and a disordered one, I used coarse-grained protein models and I did change the force parameters for each protein separately to match with the experimental measurement of the isolated proteins.