On 7/11/16 2:14 AM, elham tazikeh wrote:
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
I don't know why you would need either of these from ATB; the GROMOS force fields are already provided in GROMACS.
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?
It is a common misconception that one *needs* a .gro file; a .pdb works just fine, but certainly you can convert it if you want.
Your links don't work because they are not publicly accessible. But ATB should be very straightforward in terms of presenting you with what you need.
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?
I don't understand this. Perhaps it will be useful to follow along with a tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
-Justin
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>
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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].
