[gmx-users] Unable to neutralize my system

[Justin A. Lemkul]

Quoting namita at ncbs.res.in:

> Thanks for the suggestions but just to make my problem more clear....
>
> The "genion" command that I used is:
>
> /opt/gromacs/bin/genion_mpi -s em.tpr -o ce_myoII_frag0_neu.gro -g
> genion.log -np 2 -pname Na+
>
> And the topology file is:
>
> Before adding ions:
>
> [ molecules ]
> ; Compound        #mols
> Protein             1
> SOL           2818598
>
> After adding ions: (modified)
>
> [ molecules ]
> ; Compound        #mols
> Protein             1
> SOL           2818600
> NA+                 2

There's the problem.  Think about it - you just replaced two water molecules
with two Na+, but instead you've added two more water molecules, on top of
adding your ions.

-Justin

>
>
>
>
> 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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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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