[gmx-users] ffamber and ions

[Alan]

Hi List,
To people using ffamber.

I have ffamber with ions.itp modified to recognise ffamber ions. All seems
fine and working.

So, I have a protein, net charge +4 e. In the pdb file there no ions and no
water. I modify the pdb as said in ffamber instructions. All fine.
Then, I add water and hence I use genion to neutralise my system. I add 4
Cl. All fine.

However when using grompp for preparing the inputs for a minimisation, I got
a warning saying that my system is now +8 e. It happens no matter what ion I
use with ffamber (being it pos or neg, or value 2). It's like if genion were
counting only the ions and not reading the ion's charge value.

I know it's reading my modified ions.itp file because otherwise genion will
fail to process.

Has someone else seen that? Any comments?

Despite this, I can minimise and carry on MD on my system. Is there any
other to definitely know if GMX is computing the right charge values?

Many thanks in advance.
Cheers,
Alan

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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