[gmx-users] ATB server (charge assign)

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================