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

Mark Abraham mark.j.abraham at gmail.com
Thu Aug 20 21:00:41 CEST 2015


Yes, see pdbgmx -h about merge. Probably you want -merge interactive
-chainsep id


On Thu, Aug 20, 2015 at 8:39 PM Jorge Fernandez de Cossio Diaz <
cossio at cim.sld.cu> wrote:

> 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,
> cossio
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