Hi Gustavo,
So funny, I love the "what could go wrong"! Of course you know the answer
is "everything".
Let's talk offlist and how to Frankenstein the model. You just have to
watch the atom types.
Carlos
On Wed, Oct 23, 2019, 3:22 PM Gustavo Seabra <gustavo.seabra.gmail.com>
wrote:
> Hi all,
>
>
>
> I'd appreciate some input from you about this possibility. I need to
> simulate a protein that has one post-translational modification. I found
> the
> ForceField_PTM by the Floudas group (http://ares.tamu.edu/FFPTM/) that
> includes parameters for the modification I need (S-palmitoylcysteine), but
> the derivation methodology of ForceField_PTM is based on FF03, while the
> recommended Amber's primary FF is FF14SB. So, the way I see there are 2
> possibilities:
>
>
>
> 1. I try and derive FF14SB-compatible parameters for this residue, or
>
> 2. I use FF14SB and use the ForceField_PTM only for this one residue.
> (What could go wrong, right?)
>
>
>
> So, I wonder if anyone here has experience in this area of combining those
> force fields. How different are they? How bad would it be to combine them?
>
>
>
> Thanks a lot!
>
> Gustavo Seabra.
>
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Received on Wed Oct 23 2019 - 15:30:02 PDT
