Dear Justin thanks for your good advise as you're mentioned, i must include necessary file next to other force field files in my directory my version of gromaces is 4.6.5, and my force field is gromos 53a6
1-concerning below message, which ones is appropriate for me? Gromacs3.x.x-4.0.x 53a6-54a7 or Gromacs 4.5.x-5.x.x53a6 2-also, United-Atom PDB (original geometry) <https://atb.uq.edu.au/download.py?ffVersion=53A6&file=pdb_uniatom_unoptimised&hash=HEAD&outputType=top&molid=26014> will be (*.pdb ) and needs to editconf to convert ( *.gro)...coordinate file and GROMACS G53A6FF United-Atom (ITP file) <https://atb.uq.edu.au/download.py?ffVersion=53A6&file=rtp_uniatom&hash=HEAD&outputType=top&molid=26014> will be (*.itp)....topology file Is it right? 3-coud you please tell me, when i should get those files (*.pdb and *.itp)? before include proposed new files in my directory or after that? Regards elham Warning! This molecule contains non-standard atom types not included in the standard GROMOS 53A6 and 54A7 forcefield. To use these atom types the internal GROMACS parameter files must be updated. These can be downloaded using the link below. Instructions on where to place (and how to use) the files are provided in the README file included in the archive. Gromacs 3.x.x-4.0.x 53a6 - 54a7 <https://atb.uq.edu.au/forcefield_files/atb_gromacs/3/top_atb.tar.gz> Gromacs 4.5.x-5.x.x 53a6 <https://atb.uq.edu.au/forcefield_files/atb_gromacs/5/gromos53a6_atb.ff.tar.gz> -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
