[gmx-users] Re: ffamber and ions

[Alan]

Answering my self:

My ions.itp file was wrong. The correction is:

[ atoms ]
; id    type          resnr   residue     atom    cgnr   charge    mass
1       amber99_30      1       Cl         Cl       1     -1       35.45000
#endif

and so on.

Since I got my ions.itp from amber_ions.txt from
http://www.somewhereville.com/?p=114 it's also wrong there.

Basically, the error is that column cgnr is exchanged with column charge.

"Caveat Emptor"

Cheers,
Alan

On Thu, Jul 3, 2008 at 7:44 AM, Alan <alanwilter at gmail.com> wrote:
> 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<<



-- 
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<<