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.
Mark
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