[gmx-users] After solvation and before adding ions, number of molecules does not agree even though number of H2O molecules

[Justin Lemkul]

On 1/6/15 2:45 PM, Thomas Lipscomb wrote:
> Dear Justin,
> Message: 2
> Date: Mon, 05 Jan 2015 18:17:19 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] After solvation and before adding ions,
>      number of molecules does not agree even though number of H2O molecules
>      does
> Message-ID: <54AB1B7F.7090706 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
> On 1/5/15 5:21 PM, Thomas Lipscomb wrote:
>> Dear gmx-users,
>> I am trying to simulate a Maximin 3 antimicrobial peptide inserted into a membrane.
>> The top of this tutorial page:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/04_ions.html
>>
>> Has this command (though I changed the name of system_solv.gro to model1_solv.gro):
>> /usr/local/gromacs/bin/gmx grompp -f ions.mdp -c model1_solv.gro -p topol.top -o ions.tpr
>> Which causes this error:
>> -------------------------------------------------------Program gmx, VERSION 5.0.1Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/grompp.c, line: 603
>> Fatal error:number of coordinates in coordinate file (model1_solv.gro, 12266)            does not match topology (topol.top, 11116)For more information and tips for troubleshooting, please check the GROMACSwebsite athttp://www.gromacs.org/Documentation/Errors-------------------------------------------------------
>> I know that this is a common error after solvation:http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>>
>> So I checked the number of atoms in the topol.top file:
>> [ molecules ]; Compound        #molsProtein_chain_A    1SOL              3625
>
> If you have 3 peptides, shouldn't you have 3 molecules of your protein?
>
>> model1_solv.gro agrees that there are 3625 water molecules.
>>
>> I know that model1_solv.gro is the "the true value" that topol.top has to agree with:http://www.researchgate.net/post/How_do_you_match_the_number_of_coordinates_in_the_coordinate_files_topoltop_and_solvgro_in_a_protein_ligand_complex_using_Gromacs
>>
>> But I do not know what to do to fix the topol.top file to make it agree with model1_solv.gro.  Topol.top is missing 12266-11116 = 1150 molecules (or is it atoms?).
>
> -------------------------------------------------------------------------------------------
>>   It's atoms.  In [molecules], you specify exactly that - how many of each
>>   [moleculetype] there are; grompp expands the information into number of atoms.
>>
>>   -Justin
>
>
>
> Yes but I do not know how to fix the number of coordinates, because:
> This is what it is supposed to look like:[ molecules ]
> ; Compound   #mol
> Protein      1
> SOL          10189
> NA+          10
> But I already checked that SOL has the correct number of water molecules, I have not added ions yet so NA+ does not apply, and I have only 1 protein as I should.  So I cannot find anything in [molecules] to fix.
>
>
> So now I am looking at [ moleculetype ] in topol.top:
> [ moleculetype ]; Name            nrexclProtein_chain_A     3
> [ atoms ]
>
>
>
> [atoms] is really big so I don't know how to look through it to add the 1150 missing coordinates.
> model1_solv.gro
>

Given that the number of atoms in disagreement between coordinates and topology 
(1150) is exactly the size of one of your peptides, I'd be willing to bet that 
that's your issue.

-Justin

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> | model1_solv.groShared with Dropbox |
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> topol.top
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> | topol.topShared with Dropbox |
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> | View on www.dropbox.com | Preview by Yahoo |
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>
> Sincerely,Thomas
>

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

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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