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

Justin Lemkul jalemkul at vt.edu
Tue Jan 6 00:17:31 CET 2015

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 at http://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 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


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