[gmx-users] distorted structure

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 30 11:01:37 CEST 2011

On 30/03/2011 7:50 PM, Olga Ivchenko wrote:
> Dear gromacs users,
> I want to simulate small molecule - choline which is not neutral, it 
> has uncompensated positive charge. When I transform mol2 file to pdb 
> structure looks distorted (not correct) in VMD. I added with genion to 
> the system a negative ions, but the pdb structure is still distorted. 
> Please could you advice me on this?

Either you started with a broken structure, or your conversion broke it. 
Unfortunately there's no way we can tell with this information. Either 
way, the first time you notice a problem, don't plow on regardless - 
it's a great way to waste time and resources.


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