[gmx-users] Re: strangeness in gro file

Sweta Iyer iyer at wehi.EDU.AU
Thu Sep 15 03:23:56 CEST 2011 


> 
> Hi Mark,
I did a grompp without the temperature coupling and generated a .tpr file. From that I generated a .gro file using editconf. What it looks like now is it starts numbering from 1 -29, which is where the first monomer ends, again 1-29 for the second monomer and then its continuous numbering from then on! DMPC starts from 30 and its continuous till the end of the coordinate file! This still wouldnt let me generate an index file as the numbering still overlaps between the two protein chains. :(
Would it have a made a difference if, instead of including a TER after one chain of the complex, I just changed the chain id to distinguish them as  separate entities in the original pdb file that i used to begin with? I would have thought it shouldnt make a difference and has nothing to do with this issue!

Cheers
Sweta
> 
> Message: 1
> Date: Tue, 13 Sep 2011 16:12:49 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Strangeness in gro file
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E6EF461.7000900 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> On 13/09/2011 3:27 PM, Sweta Iyer wrote:
>> Hi all,
>> I am trying to use the g_membed tool to insert my protein into a DMPC membrane.
>> My protein is a dimer and hence I separated the two monomers by a TER card in the original pdb file before pdb2gmx step for gromacs to identify it as teo separate entities.. I then merged my protein file with that of the membrane and added water and ions to it. Then when I went ahead to make an index file I notice that the numbering of residues is not continuous in my gro file, ie, it starts from residue 1-29 of a monomer, then again 1-29 of the second monomer, 1-128 for the DMPC moleculaes and similarly for the SOL and ions as well. As a result, I cannot exactly specify residue number for my index file to specify the two protein groups as different as the residue numbers overlap. Even when i try to do it, i get an error message saying Atom 1 in multiple T-Coupling groups  Is there a way to re number them so that there is continuity or is there another way around to making the index file? I have not seen this the previously when I have made an index file. I am using gmx ver
> sion 4.5.4 and the 53a6 forcefield. I am not attaching the gro file here as it is quite lengthy.
> 
> Only atom numbering within a [moleculetype] is relative to that atom. 
> Index files need atom numbers from the whole system. These are 
> constructed from the first [molecules] entry being 1 to n, then the 
> second [molecules] entry n+1 to n+n (if that entry is the same 
> [moleculetype], etc. The numbers assigned to atoms and residues in the 
> coordinate file supplied to grompp are ignored. Only the atom and 
> molecule ordering is significant (and must match the .top).
> 
> Do a grompp using an .mdp file that does not use any index groups (e.g. 
> disable T-coupling), and pass that resulting .tpr to editconf to get a 
> coordinate file back out. I expect the atom numbering will now be from 1 
> to N where N is the number of atoms in the system. Use that coordinate 
> file to work out your index groups (with make_ndx or otherwise). Later, 
> you and grompp will be talking the same language. :)
> 
> Mark
> 
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 13 Sep 2011 11:44:52 +0530
> From: aiswarya pawar <aiswarya.pawar at gmail.com>
> Subject: Re: [gmx-users] g_dist error
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> 	<CAEa6cRC-iM1gnpyayNoyNspfviubyO8D5N_6JiuxSJwv=Zq=qg at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Mark,
> 
> the command line goes like this-
> 
> g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500
> 
> the index file has group1- a_1322 ( this is just a single atom from a
> protein. its in sidechain)
>                          group2- a_OW ( this is water atoms)
> 
> now as per the utility it should give me and output as-
> 
> t:1 1322 a 54119 OW 0.389
> 
> but am getting something different
> 
> On Tue, Sep 13, 2011 at 11:24 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 
>> On 13/09/2011 3:40 PM, aiswarya pawar wrote:
>> 
>> 
>> Hi Mark,
>> 
>> The -dist option says- print all the atoms in group 2 that are closer than
>> a certain distance to the center of mass of group 1.
>> That means it should give me the distance from OW to protein atom.
>> 
>> 
>> If you choose correct groups that are correctly defined with respect to
>> your trajectory and use a large enough distance cutoff.
>> 
>> 
>> 
>> And when am already specifying only one atom from protein ie say 1322. why
>> do i get this kind of output-
>> 
>> 
>> We can't tell. We don't know what your command line is, what's in your
>> simulation system, the contents of your index groups, or which groups you've
>> selected for which role. Clearly something is not working properly, and our
>> time constraints mean that we're going to assume you've done something
>> wrong, in the absence of evidence to the contrary.
>> 
>> Mark
>> 
>> 
>> 
>> t: 275  20230 SOL 62618 OW  0.341434 (nm)
>> t: 275  22019 SOL 67985 OW  0.171584 (nm)
>> t: 276  10768 SOL 34232 OW  0.303328 (nm)
>> t: 276  20230 SOL 62618 OW  0.325176 (nm)
>> t: 276  22019 SOL 67985 OW  0.187259 (nm)
>> t: 277  10768 SOL 34232 OW  0.306008 (nm)
>> t: 277  20230 SOL 62618 OW  0.326195 (nm)
>> t: 277  22019 SOL 67985 OW  0.181089 (nm)
>> t: 278  10768 SOL 34232 OW  0.274507 (nm)
>> t: 278  22019 SOL 67985 OW  0.292652 (nm)
>> t: 279  10618 SOL 33782 OW  0.319922 (nm)
>> t: 280  10618 SOL 33782 OW  0.330082 (nm)
>> t: 280  22019 SOL 67985 OW  0.330203 (nm)
>> t: 281  8273 SOL 26747 OW  0.278731 (nm)
>> t: 281  10618 SOL 33782 OW  0.325434 (nm)
>> t: 281  11535 SOL 36533 OW  0.200327 (nm)
>> t: 281  17036 SOL 53036 OW  0.343946 (nm)
>> t: 282  8273 SOL 26747 OW  0.256558 (nm)
>> t: 282  11535 SOL 36533 OW  0.327147 (nm)
>> t: 283  8273 SOL 26747 OW  0.165061 (nm)
>> t: 283  10618 SOL 33782 OW  0.306578 (nm)
>> t: 283  17191 SOL 53501 OW  0.333075 (nm)
>> t: 284  8273 SOL 26747 OW  0.19427 (nm)
>> t: 284  10618 SOL 33782 OW  0.321927 (nm)
>> t: 284  17191 SOL 53501 OW  0.30832 (nm)
>> 
>> 
>> 
>> 
>> On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>> 
>>> On 13/09/2011 2:27 PM, aiswarya.pawar at gmail.com wrote:
>>> 
>>> Iam -dist option because I need the distance between two groups
>>> 
>>> 
>>> That is not what g_dist -dist does. Please read g_dist -h.
>>> 
>>> 
>>>  excluding -dist gives me X,Y,Z output which I don't want.
>>> 
>>> 
>>> And other output which you do, but you have to use -o to get it. Read
>>> g_dist -h.
>>> 
>>> 
>>>  And am not specifying an -o.
>>> 
>>> 
>>> You need to specify -o to achieve your purpose. However, as I said quite
>>> a while ago, there is no value in measuring the distance between a protein
>>> phase and a water phase if they are in contact...
>>> 
>>> Mark
>>> 
>>> 
>>> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
>>> 
>>> -----Original Message-----
>>> From: "Justin A. Lemkul" <jalemkul at vt.edu> <jalemkul at vt.edu>
>>> Date: Mon, 12 Sep 2011 22:35:28
>>> To: <aiswarya.pawar at gmail.com> <aiswarya.pawar at gmail.com>; Discussion list for GROMACS users<gmx-users at gromacs.org> <gmx-users at gromacs.org>
>>> Reply-To: jalemkul at vt.edu
>>> Subject: Re: [gmx-users] g_dist error
>>> 
>>> 
>>> aiswarya.pawar at gmail.com wrote:
>>> 
>>> Even if I specify an atom say 1277 atom number to find distance against the OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even after specifying one atom from a protein why doesn't it give me the result for the SOL.
>>> 
>>> 
>>> 
>>> As was suggested several messages ago, please do NOT combine -o and -dist.  If
>>> you want to measure a distance, use -o.  If you want g_dist to print a list of
>>> atoms that satisfy some given criteria, use -dist, but not together.
>>> 
>>> -Justin
>>> 
>>> 
>>> Thanks
>>> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
>>> 
>>> -----Original Message-----
>>> From: "Justin A. Lemkul" <jalemkul at vt.edu> <jalemkul at vt.edu>
>>> Sender: gmx-users-bounces at gromacs.org
>>> Date: Mon, 12 Sep 2011 07:52:54
>>> To: Discussion list for GROMACS users<gmx-users at gromacs.org> <gmx-users at gromacs.org>
>>> Reply-To: jalemkul at vt.edu,
>>> 	Discussion list for GROMACS users <gmx-users at gromacs.org> <gmx-users at gromacs.org>
>>> Subject: Re: [gmx-users] g_dist error
>>> 
>>> 
>>> 
>>> aiswarya pawar wrote:
>>> 
>>> hi Justin,
>>> 
>>> As far i referred the OW,HW1 etc are water atoms so how can it be
>>> distance between the SOL protein atoms, instead it is SOL water atoms.
>>> 
>>> 
>>> The printed distance indicates that there is a certain water molecule that is
>>> just over 2 hydrogen bonding lengths away from your protein's backbone.  Sounds
>>> normal to me.
>>> 
>>> -Justin
>>> 
>>> 
>>> Thanks
>>> 
>>> On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu> <jalemkul at vt.edu>> wrote:
>>> 
>>> 
>>> 
>>>    aiswarya pawar wrote:
>>> 
>>>        Hi Users,
>>> 
>>>        Am using g_dist to find the distance between water and protein.
>>>        but my output has the values of SOL-water distance.
>>> 
>>>        t: 1  136 SOL 2336 OW  0.772373 (nm)
>>> 
>>> 
>>>    This is not a water-water distance, it is the output of the -dist
>>>    option telling you that water molecule 136 has its OW atom at
>>>    0.7723273 nm from whatever your reference group is.
>>> 
>>>    -Justin
>>> 
>>>    --
>>>    ==============================__==========
>>> 
>>>    Justin A. Lemkul
>>>    Ph.D. Candidate
>>>    ICTAS Doctoral Scholar
>>>    MILES-IGERT Trainee
>>>    Department of Biochemistry
>>>    Virginia Tech
>>>    Blacksburg, VA
>>>    jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) 231-9080
>>>    http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>>>    <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> 
>>>    ==============================__==========
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>> 
>> 
>> 
>> 
>> 
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