Thanks for the quick reply, I have already done that, and GROMACS, in all other cases, knows it is DNA, as it automatically forms the bonds with other residues.
it is only when it makes its index files that it doesnt know that my residue is DNA. Cheers Will Date: Sat, 12 Feb 2011 03:33:15 +1100 From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Subject: Re: [gmx-users] Add custom residue to DNA index group Message body On 12/02/2011 3:14 AM, william Stebbeds wrote: Hi Folks, I have added a custom DNA residue to the amber99sb ff, and everything works perfectly, (thanks to Justin!). The residue is incorporated perfectly into the sequence, with no abnormal events during simulations. I have updated all the files to include the new residue. I have since realised, when using g_rms, that my custom residue is not included in the default DNA index group, and appears as a group on its own. Is there a way of making gromacs understand that this residue is DNA when it makes the index files? I am not using make_ndx, I just let gromacs split the groups. Thanks in advance Will - Cranfield University You need to arrange for the tools to access a modified form of share/gromacs/top/residuetypes.dat with your custom residue suitably classified. I understand you can copy that file to your working directory and modify it there, and GROMACS will use the local copy. Mark -- 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
-- 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