Okay,okay, I give in. To settle this again, I looked it up, and among the options to -chainsep is 'interactive'. If you use that you're prompted whether or not to separate at the breaks pdb2gmx detects. That allows you to merge chains. I guess there'd be sense in just having an option 'no' to merge everything, but that's for the developers to pick up ;)
Cheers, Tsjerk On Thu, May 24, 2012 at 10:28 PM, Francesca <francesca.stanzi...@unina.it> wrote: > I had the same problem and I didn't find any way to do it. So i created new > residues for the terminals, and I added them to the forcefields files. > Example: if my first COOH terminal was a SER i created a SERT residues and I > used the COOH values taken from ASP , and the same procedure was used for > the next Nterminal...in that way I have a SERT in the list of amminoacids > and when you process the pdb2gmx you have 1moleculetype, but you have 3 > different chains each with its terminals. Be careful to use correct values > and add these residues to the list of amminoacids in the forcefield > directory. I used that method and I could apply the distance restraints. > > Cheers, > Francesca > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/One-molculetype-for-3-proteins-tp4997727p4997736.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
