[gmx-users] Broken protein chain: "WARNING: Listed nonbonded interaction between particles ..."

Jorge Fernandez de Cossio Diaz cossio at cim.sld.cu
Thu Aug 20 20:38:59 CEST 2015

Hi all,

I have a PDB file containing two proteins. One of the proteins has a long stretch of missing residues. When I try to energy-minimize it, I get the following:

WARNING: Listed nonbonded interaction between particles 2897 and 2908
at distance 3f which is larger than the table limit 3f nm.

Now, it turns out that atoms 2897 and 2908 belong to the residues between which the missing sequence lies. They are very far apart (because the missing stretch is quite long), so I don't think there should be any interaction between them. However, this WARNING seems to be saying that for some reason, the topology generated included an interaction between them, probably because it interpreted that since the two residues are consecutive in the PDB file, they are bonded (which they aren't, because of the missing residues).

After trying some things, I realized that if I remove the option "-chainsep id" from pdb2gmx when I generate the topology, I don't get this warning. Instead, I get a bunch of topology files, each corresponding to a fragment of each chain, instead of a topology per chain. This is very hard to deal with, because, for example, if I want to make a position restrain on the backbone of each chain, I have to keep track of each fragment separately.

Is there a way to fix the WARNING above without having to remove the option "-chainsep id" from pdb2gmx?

Thanks. Best,


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