[gmx-users] Broken protein chain: "WARNING: Listed nonbonded

Justin Lemkul jalemkul at vt.edu
Thu Aug 20 23:55:24 CEST 2015 


On 8/20/15 5:21 PM, Jorge Fernandez de Cossio Diaz wrote:
> Note that I am adding position restrains to fix all the termini of the incomplete fragments. Shouldn't that take care of the missing residues?
>

If there's a bond between residues that are separated by a large gap, the 
magnitude of the bonded force is going to be orders of magnitude larger than any 
restraint force.

You need to fix your missing residues.  No amount of hacking or trickery is 
going to give you a sensible result here.

-Justin

> ------------------------------
>
> Message: 5
> Date: Thu, 20 Aug 2015 20:29:42 +0000
> From: Jorge Fernandez de Cossio Diaz <cossio at cim.sld.cu>
> To: "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:
>          <FCD5150195922740996C04D9F8A6DFBB52C4C679 at Cimex2010MB1.cim.sld.cu>
> Content-Type: text/plain; charset="us-ascii"
>
> 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?
>
> ------------------------------
>
> 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]
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 20 Aug 2015 16:40:27 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Broken protein chain: "WARNING: Listed
>          nonbonded interaction between particles ..."
> Message-ID: <55D63B3B.6040702 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> 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
>
> ==================================================
>
>
> ------------------------------
>
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> End of gromacs.org_gmx-users Digest, Vol 136, Issue 103
> *******************************************************
> ---------------------------------------------------
>
> [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

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

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