Hi, To set things straight a bit.
>> "If you are using ion-related GROMACS tools, such as genion, you will need >> to enter the AMBER ion definition to the ions.itp file in the "top" >> directory of the GROMACS distribution." > > This isn't too tough, as all the parameters for the ions are included with > the Amber ports, but genion needs them to be in the ions.itp (or other > suitable) file. This has nothing to do with genion. Genion just uses the names for ions that are given (either explicitly or as default) with options -pname and -nname. When the ions occur in the system (under [ system ] in the .top file), they have to be defined somewhere as moleculetypes. Otherwise grompp will complain; no other program. ions.itp is just an intuitive place for these moleculetype definitions. Please inform yourself well regarding the way gromacs handles topologies. Check chapter 5 of the manual. This goes double when answering posts on such topics. Although such efforts are commonly appreciated, (partly) wrong information may send the original poster further off. >> Dear gromacs users, >> I am using genion command to add ions to .tpr file which >> was made for protein by use of amber03 force field. >> In intial pdb file N-terminal amino acid is NHIE, but genion changes it to >> NHI, which isnot recognized by next pdb2gmx. >> This is not a big problem , but it looks is a little bit like a bug. Justin answered this part of the question. For a suitable scheme to set up your simulations, you may want to check http://www.nmr.chem.uu.nl/~tsjerk/course/molmod/md.html Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
