If you use TER lines between anything within the residue, try removing them.
Else you could just define 0-energy bonds, except you'd have to do the
same with angles and dihedrals, which could be messy depending on the
cluster.
If the Fe is the only thing unbonded in reality, I suspect you're better
(e.g. within the ff spec) defining the other bonds anyway, and then the
Fe can be a separate molecule/atom and if desired you can also use
simple distance potentials without getting sucked into angles and dihedrals.
Bill
On 12/5/19 9:08 PM, David Sáez wrote:
> Dear Amber community:
>
> If I build a .lib file for a FeS cluster using only charges, is it
> mandatory to include bonds between atoms to make the set connected?
>
> Once created the global topology of my system, I am getting a warning from
> CPPTRAJ saying that multiple molecules share the same residue number (the
> cluster is a unique residue). I think it is happening because I did not
> create any bond within the cluster in XLeap, as I only included coulomb
> interactions between the constituent atoms...
>
>
> Thanks in advance.
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Received on Thu Dec 05 2019 - 21:30:02 PST
