[gmx-users] ffamber and ions

Alan alanwilter at gmail.com
Thu Jul 3 08:44:32 CEST 2008

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.

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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