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

Thomas Lipscomb linuxborg2 at yahoo.com
Mon Jan 5 23:21:56 CET 2015

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
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?).



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