[gmx-users] ffamber and ions

[Vigneshwar Ramakrishnan]

hi Alan,

Can you show us your modified ions.itp file (just the Cl part) and the exact
command options you used for genion?
Thanks,
Vignesh
On Thu, Jul 3, 2008 at 2:44 PM, 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<<
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
R.Vigneshwar
Graduate Student,
Dept. of Chemical & Biomolecular Engg,
National University of Singapore,
Singapore

"Strive for Excellence, Never be satisfied with the second Best!!"

"The rewards of sincere resolves are highs money can never buy!"
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080703/5cc2d606/attachment.html>