[gmx-users] Protein-ligand - genion error

[Justin Lemkul]

On 8/10/12 1:05 PM, Ankita naithani wrote:
> Dear All,
>
> I have been trying to perform simulation for a Protein and Ligand
> complex. However, when I run genion, I get an error "The solvent group
> SOL is not continuous: index[37530=23341, index[3754]=23606.
>
> I remember reading someone posting a similar problem and the solution
> was provided, according to which we need to manipulate the co-ordinate
> file and topology file. But, the problem is I really cannot understand
> at the moment as to what exactly changes I should make in order to run
> it and rectify this error.  I would be really grateful if someone
> could help me and let me know as to what exactly and how I need to
> incorporate the changes. Also, the co-ordinate file, should the
> changes be made to the one obtained after running the genbox step?
>

In the coordinate file, you'll find lines for SOL, then something else, then 
more SOL.  Your SOL lines need to be continuous, so you have to cut out whatever 
is breaking the two solvent blocks, put it either before or after SOL, and then 
make sure the [molecules] section of the topology agrees with contents of the 
new coordinate file in terms of number of molecules and order of appearance.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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