[gmx-users] Re: ffamber and ions
alanwilter at gmail.com
Tue Jul 8 10:40:57 CEST 2008
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
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.
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.
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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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