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 <[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<< -- 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
