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 <[EMAIL PROTECTED]> 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@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 [EMAIL PROTECTED] > 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!"
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