[gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters

[Nikolaos Michelarakis]

Dear All,

First, I would like to say that I have started using GROMACS during this
last month so please take that in mind when answering.

I am trying to run an MD simulation of an enzyme which contains some non
standard residues such as a tungsten metal ion and some other cofactors. I
understand that I need to create the topology and find the parameters for
these non-standard residues. Reading the manual I saw about .itp files and,
correct me if I'm wrong, but it's my understanding that these are used for
parts of the topology which are not bonded or intergrated in the structure
that is being simulated. My question is how do I include these bonded parts
in the simulation?

My second question, someone has already developed a topology and some
parameters for this structure but in CHARM. I tried using one of the two
scripts available online to convert them to GROMACS but to no avail. Is
there a way to automatically do this or will I have to go all over it by
hand?

Thank you very much in advance!

Regards,
Nicholas