[gmx-users] Re: ffamber and ions

[Damian Gregory Allis Ph.D.]

For what it may be worth, the http://www.somewhereville.com/?p=114  
page has had its ion.itp content corrected and, hopefully, it is now a  
little less useless than it was yesterday. Having fought a bit with  
the install process myself, I hope people find the ffamber/gromacs  
page of use and if they find errors or concerns to please bring them  
up (thanks Alan!).

Damian Allis

Locale : www.somewhereville.com
Delivery : damian at somewhereville.com
  Skype : somewhereville
AOL IM  : swville

On Jul 8, 2008, at 4:40 AM, Alan wrote:

> 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<<
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#8^(=)+<, ph.d.

p.s. Damian apologizes for the delay.
p.p.s. Have you backed up lately?

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