Hi List,<div><br></div><div>To people using ffamber.</div><div><br></div><div>I have ffamber with ions.itp modified to recognise ffamber ions. All seems fine and working.</div><div><br></div><div>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.</div>
<div>Then, I add water and hence I use genion to neutralise my system. I add 4 Cl. All fine.</div><div><br></div><div>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.</div>
<div><br></div><div>I know it's reading my modified ions.itp file because otherwise genion will fail to process.</div><div><br></div><div>Has someone else seen that? Any comments?</div><div><br></div><div>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?</div>
<div><br></div><div>Many thanks in advance.<br clear="all">Cheers,</div><div>Alan</div><div><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge.<br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<
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