Re: [AMBER] Warning: 2 or more molecules (3 and 4) share residue numbers (1003).

From: Bill Ross <>
Date: Thu, 5 Dec 2019 21:27:39 -0800

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

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.


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
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