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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