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

[Justin Lemkul]

On 8/20/15 4:29 PM, Jorge Fernandez de Cossio Diaz wrote:
> Tried using -merge interactive -chainsep id on pdb2gmx, but I still get the same WARNING:
>
> WARNING: Listed nonbonded interaction between particles 2897 and 2908
> at distance 3f which is larger than the table limit 3f nm.
>
> The energy minimization step prints this as a warning and proceeds, but when I try to equilibrate the system later, the warning becomes an error and it doesn't let me proceed, so this seems to be important. Also, it doesn't make sense to me that 2897 and 2908 are interacting, because even though they are consecutive (because of missing residues), they are very far apart in space.
>
> So why is it that when I put the fragments into the same chain, the topology creates this spurious interaction?
>

Because you're ignoring something physically relevant - you have missing 
residues!  pdb2gmx certainly gave "long bond" warnings when you produced the 
topology.  You need to model in the missing residues, otherwise the structure is 
useless to you.

-Justin

> ------------------------------
>
> Message: 4
> Date: Thu, 20 Aug 2015 19:00:29 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org, "gromacs.org_gmx-users at maillist.sys.kth.se"
>          <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Broken protein chain: "WARNING: Listed
>          nonbonded interaction between particles ..."
> Message-ID:
>          <CAMNuMARXoFeT_HN0J57y2pt=gzatNzgB+11ASgpm6dxVYQ3U-w at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Yes, see pdbgmx -h about merge. Probably you want -merge interactive
> -chainsep id
>
> Mark
>
> 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
>> ---------------------------------------------------
> ---------------------------------------------------
>
> [http://5.cim.co.cu/cim.gif]
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================