[gmx-users] Unable to neutralize my system

[Alan Dodd]

You haven't edited your topology files correctly.  If changing the number of ions has not resulting in a change of charge, I'd suggest you haven't added the ions in right; otherwise, I suspect it's something to do with the number of waters.  Particularly as the error in coordinates vs. topology is divisible by 3.

----- Original Message ----
From: "namita at ncbs.res.in" <namita at ncbs.res.in>
To: gmx-users at gromacs.org
Sent: Thursday, May 8, 2008 11:34:20 AM
Subject: [gmx-users] Unable to neutralize my system

Dear All

When I run the command "genion" specifying the number n type of chrges to
be added, it works fine. I also have made changes in my topology file. But
somwhow when I run the "grompp" after that it gives me the following
error...

processing topology...
Generated 380 of the 1326 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 2 bonded neighbours for SOL 2818600
Excluding 1 bonded neighbours for Na+ 2
NOTE:
  System has non-zero total charge: -2.399999e+01

processing coordinates...
-------------------------------------------------------
Program grompp_mpi, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (ce_myoII_frag0_neu.gro, 8461523)
            does not match topology (ce_myoII_frag0.top, 8461535)
-------------------------------------------------------

I tried adding 2 and 3 ions to the system. But it seems to give the same
error. Could someone help?

Thanks
Namitha Mohandas

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