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

[Thomas Lipscomb]

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

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topol.top

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Sincerely,Thomas